From 215b0fc5b3eaed3d50aa92e993d550ad16a5f3cc Mon Sep 17 00:00:00 2001
From: Vadym <vadym.ivanchuk@scilifelab.se>
Date: Tue, 6 Aug 2024 11:33:00 +0200
Subject: [PATCH 01/38] Bump tiddit version

---
 BALSAMIC/containers/varcall_py3/varcall_py3.yaml | 2 +-
 docs/balsamic_methods.rst                        | 2 +-
 docs/bioinfo_softwares.rst                       | 2 +-
 tests/test_data/config.json                      | 2 +-
 tests/test_data/config_pon.json                  | 2 +-
 5 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/BALSAMIC/containers/varcall_py3/varcall_py3.yaml b/BALSAMIC/containers/varcall_py3/varcall_py3.yaml
index 4f106103e..7b63b41e4 100644
--- a/BALSAMIC/containers/varcall_py3/varcall_py3.yaml
+++ b/BALSAMIC/containers/varcall_py3/varcall_py3.yaml
@@ -163,7 +163,7 @@ dependencies:
   - svdb=2.8.1
   - sysroot_linux-64=2.12
   - tabix=1.11
-  - tiddit=3.3.2
+  - tiddit=3.8.0
   - tk=8.6.12
   - tktable=2.10
   - toolz=0.12.0
diff --git a/docs/balsamic_methods.rst b/docs/balsamic_methods.rst
index 783e2f1c5..c8a37f990 100644
--- a/docs/balsamic_methods.rst
+++ b/docs/balsamic_methods.rst
@@ -36,7 +36,7 @@ The final BAM is quality controlled using WgsMetricsAlgo and CoverageMetrics fro
 Results of the quality controlled steps were summarized by MultiQC v1.12 :superscript:`7`.
 Small somatic mutations (SNVs and INDELs) were called for each sample using Sentieon TNscope :superscript:`16`.
 The called-variants were also further second filtered using the criteria (DP(tumor,normal) >= 10; AD(tumor) >= 3; AF(tumor) >= 0.05, Maximum AF(tumor < 1;  GNOMADAF_popmax <= 0.001; normalized base quality scores >= 20, read_counts of alt,ref alle > 0).
-Structural variants were called using Manta v1.6.0 :superscript:`9`, Delly v1.0.3 :superscript:`10` and TIDDIT v3.3.2 :superscript:`12`.
+Structural variants were called using Manta v1.6.0 :superscript:`9`, Delly v1.0.3 :superscript:`10` and TIDDIT v3.8.0 :superscript:`12`.
 Copy number variations (CNV) were called using ascatNgs v4.5.0 :superscript:`17` (tumor-normal), Delly v1.0.3 :superscript:`10` and CNVpytor v1.3.1 :superscript:`22` (tumor-only) and converted from CNV to deletions (DEL) and duplications (DUP).
 The structural variant (SV) calls from Manta, Delly, TIDDIT, ascatNgs (tumor-normal) and CNVpytor (tumor-only) were merged using SVDB v2.8.1 :superscript:`12`
 The clinical set of SNV and SV is also annotated and filtered against loqusDB curated frequency of observed variants (frequency < 0.01) from non-cancer cases and only annotated using frequency of observed variants from cancer cases (somatic and germline).
diff --git a/docs/bioinfo_softwares.rst b/docs/bioinfo_softwares.rst
index c49b34844..3e752021a 100644
--- a/docs/bioinfo_softwares.rst
+++ b/docs/bioinfo_softwares.rst
@@ -146,7 +146,7 @@ tiddit
 ~~~~~~
 :Source code: `Github` `<https://github.com/SciLifeLab/TIDDIT>`_
 :Article: `F1000Res` `<https://pubmed.ncbi.nlm.nih.gov/28781756/>`_
-:Version: `3.3.2`
+:Version: `3.8.0`
 
 vardict
 ~~~~~~~
diff --git a/tests/test_data/config.json b/tests/test_data/config.json
index ec9a4f511..889577f85 100644
--- a/tests/test_data/config.json
+++ b/tests/test_data/config.json
@@ -205,7 +205,7 @@
     "gatk": ["3.8"],
     "samtools": ["1.15.1", "1.9"],
     "svdb": ["2.8.1"],
-    "tiddit": ["3.3.2"],
+    "tiddit": ["3.8.0"],
     "vardict": ["2019.06.04"],
     "somalier": ["0.2.16"],
     "delly": ["1.0.3"],
diff --git a/tests/test_data/config_pon.json b/tests/test_data/config_pon.json
index 7ef3dd26b..cbff98963 100644
--- a/tests/test_data/config_pon.json
+++ b/tests/test_data/config_pon.json
@@ -70,7 +70,7 @@
     "bwa": ["0.7.17"],
     "gatk": ["3.8"],
     "svdb": ["2.8.1"],
-    "tiddit": ["3.3.2"],
+    "tiddit": ["3.8.0"],
     "vardict": ["2019.06.04"],
     "csvkit": ["1.0.7"],
     "fastp": ["0.23.2"],

From 9b93b9ecfb18683a4ddadcd0b9c55a7b99539125 Mon Sep 17 00:00:00 2001
From: Vadym <vadym.ivanchuk@scilifelab.se>
Date: Tue, 6 Aug 2024 11:34:07 +0200
Subject: [PATCH 02/38] CHANGELOG

---
 CHANGELOG.rst | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index b05912b31..73e7284c1 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -13,6 +13,7 @@ Changed:
 * `SLEEP_BEFORE_START` to 600s https://github.com/Clinical-Genomics/BALSAMIC/pull/1372
 * Updated Multiqc to version 1.22.3 https://github.com/Clinical-Genomics/BALSAMIC/pull/1441
 * Upgrade `vcf2cytosure` version to 0.9.1 and remove hardcoded versions https://github.com/Clinical-Genomics/BALSAMIC/pull/1456
+* Upgrade `TIDDIT` version to 3.8.0 https://github.com/Clinical-Genomics/BALSAMIC/pull/1469
 
 Removed:
 ^^^^^^^^

From ebaef449b4d0987dba4e3510580b543891720146 Mon Sep 17 00:00:00 2001
From: Vadym <vadym.ivanchuk@scilifelab.se>
Date: Tue, 6 Aug 2024 11:50:12 +0200
Subject: [PATCH 03/38] changelog

---
 CHANGELOG.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index 73e7284c1..e66a08736 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -13,7 +13,7 @@ Changed:
 * `SLEEP_BEFORE_START` to 600s https://github.com/Clinical-Genomics/BALSAMIC/pull/1372
 * Updated Multiqc to version 1.22.3 https://github.com/Clinical-Genomics/BALSAMIC/pull/1441
 * Upgrade `vcf2cytosure` version to 0.9.1 and remove hardcoded versions https://github.com/Clinical-Genomics/BALSAMIC/pull/1456
-* Upgrade `TIDDIT` version to 3.8.0 https://github.com/Clinical-Genomics/BALSAMIC/pull/1469
+* Upgrade `TIDDIT` version to 3.8.0 https://github.com/Clinical-Genomics/BALSAMIC/pull/1470
 
 Removed:
 ^^^^^^^^

From 4298b857d0b1b1c81fa54dfe9c66836e0433d4ef Mon Sep 17 00:00:00 2001
From: Vadym <vadym.ivanchuk@scilifelab.se>
Date: Tue, 6 Aug 2024 12:00:45 +0200
Subject: [PATCH 04/38] Use WORKDIR

---
 BALSAMIC/containers/varcall_py3/Dockerfile | 28 +++++++++++++---------
 1 file changed, 17 insertions(+), 11 deletions(-)

diff --git a/BALSAMIC/containers/varcall_py3/Dockerfile b/BALSAMIC/containers/varcall_py3/Dockerfile
index 141861c72..638bb3a8a 100644
--- a/BALSAMIC/containers/varcall_py3/Dockerfile
+++ b/BALSAMIC/containers/varcall_py3/Dockerfile
@@ -1,22 +1,28 @@
 FROM continuumio/miniconda3:4.10.3-alpine
 
-LABEL base.image="continuumio/miniconda3:4.10.3-alpine"
-LABEL about.home="https://github.com/Clinical-Genomics/BALSAMIC"
-LABEL about.documentation="https://balsamic.readthedocs.io/"
-LABEL about.license="MIT License (MIT)"
-LABEL about.description="Bioinformatic analysis pipeline for somatic mutations in cancer"
+LABEL base.image="continuumio/miniconda3:4.10.3-alpine" \
+      about.home="https://github.com/Clinical-Genomics/BALSAMIC" \
+      about.documentation="https://balsamic.readthedocs.io/" \
+      about.license="MIT License (MIT)" \
+      about.description="Bioinformatic analysis pipeline for somatic mutations in cancer"
 
 ENV PATH="/opt/conda/bin/:${PATH}"
 
+# Install necessary packages
 RUN apk add --no-cache bash gcc git
 
-ARG WORK_DIR=project
 ARG CONTAINER_NAME
 
-# Copy all project files
-COPY . /${WORK_DIR}
+# Set the working directory
+WORKDIR /project
 
-RUN cd /${WORK_DIR}/BALSAMIC/containers/${CONTAINER_NAME}/ && /bin/sh ${CONTAINER_NAME}.sh ${CONTAINER_NAME}
+# Copy all project files to WORKDIR
+COPY . .
 
-# Clean work environment
-RUN rm -rf /${WORK_DIR:?} && conda clean --all --yes
+# Execute the container specific script
+WORKDIR /project/BALSAMIC/containers/${CONTAINER_NAME}
+RUN /bin/sh ${CONTAINER_NAME}.sh ${CONTAINER_NAME}
+
+# Clean up work environment
+WORKDIR /
+RUN rm -rf /project && conda clean --all --yes

From af3a17777bcc294890e56ccd1ce42109a72499f0 Mon Sep 17 00:00:00 2001
From: Vadym <vadym.ivanchuk@scilifelab.se>
Date: Thu, 8 Aug 2024 13:24:15 +0200
Subject: [PATCH 05/38] Upgrade NIM somalier

---
 BALSAMIC/containers/somalier/Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/BALSAMIC/containers/somalier/Dockerfile b/BALSAMIC/containers/somalier/Dockerfile
index f3a40d890..b8a679eff 100644
--- a/BALSAMIC/containers/somalier/Dockerfile
+++ b/BALSAMIC/containers/somalier/Dockerfile
@@ -6,7 +6,7 @@ LABEL about.documentation="https://balsamic.readthedocs.io/"
 LABEL about.license="MIT License (MIT)"
 LABEL about.description="Bioinformatic analysis pipeline for somatic mutations in cancer"
 
-ARG nim_version=1.6.6
+ARG nim_version=2.0.8
 
 ENV CFLAGS="-fPIC -O3"
 

From c693f6e8bb6843de6b6ad39cf64950c3bbf4a633 Mon Sep 17 00:00:00 2001
From: Vadym <vadym.ivanchuk@scilifelab.se>
Date: Thu, 8 Aug 2024 13:45:27 +0200
Subject: [PATCH 06/38] 3.7

---
 BALSAMIC/containers/varcall_py3/varcall_py3.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/BALSAMIC/containers/varcall_py3/varcall_py3.yaml b/BALSAMIC/containers/varcall_py3/varcall_py3.yaml
index 7b63b41e4..05a89fb01 100644
--- a/BALSAMIC/containers/varcall_py3/varcall_py3.yaml
+++ b/BALSAMIC/containers/varcall_py3/varcall_py3.yaml
@@ -163,7 +163,7 @@ dependencies:
   - svdb=2.8.1
   - sysroot_linux-64=2.12
   - tabix=1.11
-  - tiddit=3.8.0
+  - tiddit=3.7.0
   - tk=8.6.12
   - tktable=2.10
   - toolz=0.12.0

From 39ec175cf566e5f12b497621cc34c31799b8f534 Mon Sep 17 00:00:00 2001
From: Vadym <vadym.ivanchuk@scilifelab.se>
Date: Thu, 8 Aug 2024 14:45:47 +0200
Subject: [PATCH 07/38] bump somalier

---
 BALSAMIC/containers/somalier/Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/BALSAMIC/containers/somalier/Dockerfile b/BALSAMIC/containers/somalier/Dockerfile
index b8a679eff..bd6c2def8 100644
--- a/BALSAMIC/containers/somalier/Dockerfile
+++ b/BALSAMIC/containers/somalier/Dockerfile
@@ -41,7 +41,7 @@ RUN cd / && \
     cd ../ && rm -rf htslib bcftools
 
 RUN cd / &&    \
-    git clone -b v0.2.16 --depth 1 https://github.com/brentp/somalier.git && \
+    git clone -b v0.2.19 --depth 1 https://github.com/brentp/somalier.git && \
     cd somalier && \
     nimble install -y nimble && \
     /root/.nimble/bin/nimble install -d -y

From 3ed2dbdd3c6de28627dd5389bbcf15b5843187d2 Mon Sep 17 00:00:00 2001
From: Vadym <vadym.ivanchuk@scilifelab.se>
Date: Thu, 8 Aug 2024 15:23:23 +0200
Subject: [PATCH 08/38] slivar

---
 BALSAMIC/containers/somalier/Dockerfile | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/BALSAMIC/containers/somalier/Dockerfile b/BALSAMIC/containers/somalier/Dockerfile
index bd6c2def8..9ab0653dc 100644
--- a/BALSAMIC/containers/somalier/Dockerfile
+++ b/BALSAMIC/containers/somalier/Dockerfile
@@ -44,7 +44,8 @@ RUN cd / &&    \
     git clone -b v0.2.19 --depth 1 https://github.com/brentp/somalier.git && \
     cd somalier && \
     nimble install -y nimble && \
-    /root/.nimble/bin/nimble install -d -y
+    /root/.nimble/bin/nimble install -d -y && \
+    nimble install -y slivar
 
 RUN cd /somalier &&  \
     nim c -d:danger -d:nsb_static -d:release -d:openmp -d:blas=openblas -d:lapack=openblas -o:/usr/bin/somalier src/somalier && \

From fb11525c616ca22221ad7689babaed37daea214b Mon Sep 17 00:00:00 2001
From: Vadym <vadym.ivanchuk@scilifelab.se>
Date: Thu, 8 Aug 2024 15:29:53 +0200
Subject: [PATCH 09/38] downgrade somalier

---
 BALSAMIC/containers/somalier/Dockerfile | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/BALSAMIC/containers/somalier/Dockerfile b/BALSAMIC/containers/somalier/Dockerfile
index 9ab0653dc..9bf48272a 100644
--- a/BALSAMIC/containers/somalier/Dockerfile
+++ b/BALSAMIC/containers/somalier/Dockerfile
@@ -6,7 +6,7 @@ LABEL about.documentation="https://balsamic.readthedocs.io/"
 LABEL about.license="MIT License (MIT)"
 LABEL about.description="Bioinformatic analysis pipeline for somatic mutations in cancer"
 
-ARG nim_version=2.0.8
+ARG nim_version=1.6.6
 
 ENV CFLAGS="-fPIC -O3"
 
@@ -44,8 +44,7 @@ RUN cd / &&    \
     git clone -b v0.2.19 --depth 1 https://github.com/brentp/somalier.git && \
     cd somalier && \
     nimble install -y nimble && \
-    /root/.nimble/bin/nimble install -d -y && \
-    nimble install -y slivar
+    /root/.nimble/bin/nimble install -d -y &&
 
 RUN cd /somalier &&  \
     nim c -d:danger -d:nsb_static -d:release -d:openmp -d:blas=openblas -d:lapack=openblas -o:/usr/bin/somalier src/somalier && \

From 9f92c8ff48e1d9ac0b7be0ae7870b54d64304736 Mon Sep 17 00:00:00 2001
From: Vadym <vadym.ivanchuk@scilifelab.se>
Date: Thu, 8 Aug 2024 15:32:40 +0200
Subject: [PATCH 10/38] typo

---
 BALSAMIC/containers/somalier/Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/BALSAMIC/containers/somalier/Dockerfile b/BALSAMIC/containers/somalier/Dockerfile
index 9bf48272a..aca55e2e4 100644
--- a/BALSAMIC/containers/somalier/Dockerfile
+++ b/BALSAMIC/containers/somalier/Dockerfile
@@ -44,7 +44,7 @@ RUN cd / &&    \
     git clone -b v0.2.19 --depth 1 https://github.com/brentp/somalier.git && \
     cd somalier && \
     nimble install -y nimble && \
-    /root/.nimble/bin/nimble install -d -y &&
+    /root/.nimble/bin/nimble install -d -y
 
 RUN cd /somalier &&  \
     nim c -d:danger -d:nsb_static -d:release -d:openmp -d:blas=openblas -d:lapack=openblas -o:/usr/bin/somalier src/somalier && \

From 1d6b0b69606167fd32f4fb2d56ab7d8861713fbf Mon Sep 17 00:00:00 2001
From: Vadym <vadym.ivanchuk@scilifelab.se>
Date: Fri, 9 Aug 2024 10:42:11 +0200
Subject: [PATCH 11/38] base somalier consdkhshdsd

---
 BALSAMIC/containers/somalier/Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/BALSAMIC/containers/somalier/Dockerfile b/BALSAMIC/containers/somalier/Dockerfile
index aca55e2e4..f3a40d890 100644
--- a/BALSAMIC/containers/somalier/Dockerfile
+++ b/BALSAMIC/containers/somalier/Dockerfile
@@ -41,7 +41,7 @@ RUN cd / && \
     cd ../ && rm -rf htslib bcftools
 
 RUN cd / &&    \
-    git clone -b v0.2.19 --depth 1 https://github.com/brentp/somalier.git && \
+    git clone -b v0.2.16 --depth 1 https://github.com/brentp/somalier.git && \
     cd somalier && \
     nimble install -y nimble && \
     /root/.nimble/bin/nimble install -d -y

From 6bdb554fe39f75feecb9014ce29fe05c4dd55101 Mon Sep 17 00:00:00 2001
From: Vadym <vadym.ivanchuk@scilifelab.se>
Date: Fri, 9 Aug 2024 10:48:49 +0200
Subject: [PATCH 12/38] comment somalier

---
 BALSAMIC/containers/somalier/Dockerfile | 100 ++++++++++++------------
 1 file changed, 50 insertions(+), 50 deletions(-)

diff --git a/BALSAMIC/containers/somalier/Dockerfile b/BALSAMIC/containers/somalier/Dockerfile
index f3a40d890..e23c40406 100644
--- a/BALSAMIC/containers/somalier/Dockerfile
+++ b/BALSAMIC/containers/somalier/Dockerfile
@@ -6,54 +6,54 @@ LABEL about.documentation="https://balsamic.readthedocs.io/"
 LABEL about.license="MIT License (MIT)"
 LABEL about.description="Bioinformatic analysis pipeline for somatic mutations in cancer"
 
-ARG nim_version=1.6.6
-
-ENV CFLAGS="-fPIC -O3"
-
-RUN apk add --no-cache wget git autoconf tar xz xz-dev bzip2-dev curl curl-dev bash libzip-dev cmake openblas-dev build-base
-
-RUN mkdir -p /usr/local/include && \
-    git clone --depth 1 https://github.com/ebiggers/libdeflate.git && \
-    cd libdeflate && cmake -B build && cmake --build build && \
-    cp /libdeflate/build/libdeflate.a /usr/local/lib && cp /libdeflate/libdeflate.h /usr/local/include && \
-    cd .. && rm -rf libdeflate
-
-RUN cd / && \
-    wget -q https://nim-lang.org/download/nim-${nim_version}-linux_x64.tar.xz && \
-    tar xf nim-${nim_version}-linux_x64.tar.xz && \
-    echo 'PATH=/nim-${nim_version}/bin:$PATH' >> ~/.bashrc && \
-    echo 'PATH=/nim-${nim_version}/bin:$PATH' >> ~/.bash_profile && \
-    echo 'PATH=/nim-${nim_version}/bin:$PATH' >> /etc/environment  && \
-    rm -f nim-${nim_version}-linux_x64.tar.xz
-
-ENV PATH=/nim-${nim_version}/bin/:$PATH
-
-RUN cd / && \
-    git clone --depth 1 -b 1.15 --recursive https://github.com/samtools/htslib && \
-    cd htslib && autoheader && autoconf && \
-    ./configure --enable-s3 --enable-gcs --enable-libcurl --with-libdeflate && \
-    make -j4 CFLAGS="-fPIC -O3" install && \
-    cd ../ && \
-    git clone --depth 1 -b 1.15 --recursive https://github.com/samtools/bcftools && \
-    cd bcftools && autoheader && autoconf && \
-    ./configure --enable-s3 --enable-libcurl --with-libdeflate && \
-    make -j4 CFLAGS="-fPIC -O3" install && \
-    cd ../ && rm -rf htslib bcftools
-
-RUN cd / &&    \
-    git clone -b v0.2.16 --depth 1 https://github.com/brentp/somalier.git && \
-    cd somalier && \
-    nimble install -y nimble && \
-    /root/.nimble/bin/nimble install -d -y
-
-RUN cd /somalier &&  \
-    nim c -d:danger -d:nsb_static -d:release -d:openmp -d:blas=openblas -d:lapack=openblas -o:/usr/bin/somalier src/somalier && \
-    cp scripts/ancestry-labels-1kg.tsv / && \
-    rm -rf /somalier && somalier --help
-
-ENV somalier_ancestry_labels /ancestry_labels-1kg.tsv
-
-RUN adduser -D defaultuser
-
-USER defaultuser
+#ARG nim_version=1.6.6
+#
+#ENV CFLAGS="-fPIC -O3"
+#
+#RUN apk add --no-cache wget git autoconf tar xz xz-dev bzip2-dev curl curl-dev bash libzip-dev cmake openblas-dev build-base
+#
+#RUN mkdir -p /usr/local/include && \
+#    git clone --depth 1 https://github.com/ebiggers/libdeflate.git && \
+#    cd libdeflate && cmake -B build && cmake --build build && \
+#    cp /libdeflate/build/libdeflate.a /usr/local/lib && cp /libdeflate/libdeflate.h /usr/local/include && \
+#    cd .. && rm -rf libdeflate
+#
+#RUN cd / && \
+#    wget -q https://nim-lang.org/download/nim-${nim_version}-linux_x64.tar.xz && \
+#    tar xf nim-${nim_version}-linux_x64.tar.xz && \
+#    echo 'PATH=/nim-${nim_version}/bin:$PATH' >> ~/.bashrc && \
+#    echo 'PATH=/nim-${nim_version}/bin:$PATH' >> ~/.bash_profile && \
+#    echo 'PATH=/nim-${nim_version}/bin:$PATH' >> /etc/environment  && \
+#    rm -f nim-${nim_version}-linux_x64.tar.xz
+#
+#ENV PATH=/nim-${nim_version}/bin/:$PATH
+#
+#RUN cd / && \
+#    git clone --depth 1 -b 1.15 --recursive https://github.com/samtools/htslib && \
+#    cd htslib && autoheader && autoconf && \
+#    ./configure --enable-s3 --enable-gcs --enable-libcurl --with-libdeflate && \
+#    make -j4 CFLAGS="-fPIC -O3" install && \
+#    cd ../ && \
+#    git clone --depth 1 -b 1.15 --recursive https://github.com/samtools/bcftools && \
+#    cd bcftools && autoheader && autoconf && \
+#    ./configure --enable-s3 --enable-libcurl --with-libdeflate && \
+#    make -j4 CFLAGS="-fPIC -O3" install && \
+#    cd ../ && rm -rf htslib bcftools
+#
+#RUN cd / &&    \
+#    git clone -b v0.2.16 --depth 1 https://github.com/brentp/somalier.git && \
+#    cd somalier && \
+#    nimble install -y nimble && \
+#    /root/.nimble/bin/nimble install -d -y
+#
+#RUN cd /somalier &&  \
+#    nim c -d:danger -d:nsb_static -d:release -d:openmp -d:blas=openblas -d:lapack=openblas -o:/usr/bin/somalier src/somalier && \
+#    cp scripts/ancestry-labels-1kg.tsv / && \
+#    rm -rf /somalier && somalier --help
+#
+#ENV somalier_ancestry_labels /ancestry_labels-1kg.tsv
+#
+#RUN adduser -D defaultuser
+#
+#USER defaultuser
 

From 6db13ef36c5b6db8cb310e2cfdfd4f7e3769e41c Mon Sep 17 00:00:00 2001
From: Vadym <vadym.ivanchuk@scilifelab.se>
Date: Fri, 9 Aug 2024 10:51:36 +0200
Subject: [PATCH 13/38] :)

---
 BALSAMIC/containers/somalier/Dockerfile | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/BALSAMIC/containers/somalier/Dockerfile b/BALSAMIC/containers/somalier/Dockerfile
index e23c40406..868893c38 100644
--- a/BALSAMIC/containers/somalier/Dockerfile
+++ b/BALSAMIC/containers/somalier/Dockerfile
@@ -6,6 +6,9 @@ LABEL about.documentation="https://balsamic.readthedocs.io/"
 LABEL about.license="MIT License (MIT)"
 LABEL about.description="Bioinformatic analysis pipeline for somatic mutations in cancer"
 
+WORKDIR /app
+CMD ["sh"]
+
 #ARG nim_version=1.6.6
 #
 #ENV CFLAGS="-fPIC -O3"

From a624f243b4ec89a1b20e7d7f9f44165817a19f7f Mon Sep 17 00:00:00 2001
From: Vadym <vadym.ivanchuk@scilifelab.se>
Date: Fri, 9 Aug 2024 10:54:09 +0200
Subject: [PATCH 14/38] deactivate somalier

---
 .../docker_build_publish_develop.yml          |   2 +-
 BALSAMIC/containers/somalier/Dockerfile       | 103 +++++++++---------
 2 files changed, 51 insertions(+), 54 deletions(-)

diff --git a/.github/workflows/docker_build_publish_develop.yml b/.github/workflows/docker_build_publish_develop.yml
index fde5a4faf..4e858c8d8 100644
--- a/.github/workflows/docker_build_publish_develop.yml
+++ b/.github/workflows/docker_build_publish_develop.yml
@@ -15,7 +15,7 @@ jobs:
     strategy:
       fail-fast: true
       matrix:
-        container-name: [align_qc, annotate, ascatNgs, cadd, cnvkit, cnvpytor, coverage_qc, delly, gatk, htslib, multiqc, msisensorpro, purecn, somalier, varcall_py3, varcall_py27, vcf2cytosure]
+        container-name: [align_qc, annotate, ascatNgs, cadd, cnvkit, cnvpytor, coverage_qc, delly, gatk, htslib, multiqc, msisensorpro, purecn, varcall_py3, varcall_py27, vcf2cytosure]
     steps:
       - name: Git checkout
         id: git_checkout
diff --git a/BALSAMIC/containers/somalier/Dockerfile b/BALSAMIC/containers/somalier/Dockerfile
index 868893c38..f3a40d890 100644
--- a/BALSAMIC/containers/somalier/Dockerfile
+++ b/BALSAMIC/containers/somalier/Dockerfile
@@ -6,57 +6,54 @@ LABEL about.documentation="https://balsamic.readthedocs.io/"
 LABEL about.license="MIT License (MIT)"
 LABEL about.description="Bioinformatic analysis pipeline for somatic mutations in cancer"
 
-WORKDIR /app
-CMD ["sh"]
-
-#ARG nim_version=1.6.6
-#
-#ENV CFLAGS="-fPIC -O3"
-#
-#RUN apk add --no-cache wget git autoconf tar xz xz-dev bzip2-dev curl curl-dev bash libzip-dev cmake openblas-dev build-base
-#
-#RUN mkdir -p /usr/local/include && \
-#    git clone --depth 1 https://github.com/ebiggers/libdeflate.git && \
-#    cd libdeflate && cmake -B build && cmake --build build && \
-#    cp /libdeflate/build/libdeflate.a /usr/local/lib && cp /libdeflate/libdeflate.h /usr/local/include && \
-#    cd .. && rm -rf libdeflate
-#
-#RUN cd / && \
-#    wget -q https://nim-lang.org/download/nim-${nim_version}-linux_x64.tar.xz && \
-#    tar xf nim-${nim_version}-linux_x64.tar.xz && \
-#    echo 'PATH=/nim-${nim_version}/bin:$PATH' >> ~/.bashrc && \
-#    echo 'PATH=/nim-${nim_version}/bin:$PATH' >> ~/.bash_profile && \
-#    echo 'PATH=/nim-${nim_version}/bin:$PATH' >> /etc/environment  && \
-#    rm -f nim-${nim_version}-linux_x64.tar.xz
-#
-#ENV PATH=/nim-${nim_version}/bin/:$PATH
-#
-#RUN cd / && \
-#    git clone --depth 1 -b 1.15 --recursive https://github.com/samtools/htslib && \
-#    cd htslib && autoheader && autoconf && \
-#    ./configure --enable-s3 --enable-gcs --enable-libcurl --with-libdeflate && \
-#    make -j4 CFLAGS="-fPIC -O3" install && \
-#    cd ../ && \
-#    git clone --depth 1 -b 1.15 --recursive https://github.com/samtools/bcftools && \
-#    cd bcftools && autoheader && autoconf && \
-#    ./configure --enable-s3 --enable-libcurl --with-libdeflate && \
-#    make -j4 CFLAGS="-fPIC -O3" install && \
-#    cd ../ && rm -rf htslib bcftools
-#
-#RUN cd / &&    \
-#    git clone -b v0.2.16 --depth 1 https://github.com/brentp/somalier.git && \
-#    cd somalier && \
-#    nimble install -y nimble && \
-#    /root/.nimble/bin/nimble install -d -y
-#
-#RUN cd /somalier &&  \
-#    nim c -d:danger -d:nsb_static -d:release -d:openmp -d:blas=openblas -d:lapack=openblas -o:/usr/bin/somalier src/somalier && \
-#    cp scripts/ancestry-labels-1kg.tsv / && \
-#    rm -rf /somalier && somalier --help
-#
-#ENV somalier_ancestry_labels /ancestry_labels-1kg.tsv
-#
-#RUN adduser -D defaultuser
-#
-#USER defaultuser
+ARG nim_version=1.6.6
+
+ENV CFLAGS="-fPIC -O3"
+
+RUN apk add --no-cache wget git autoconf tar xz xz-dev bzip2-dev curl curl-dev bash libzip-dev cmake openblas-dev build-base
+
+RUN mkdir -p /usr/local/include && \
+    git clone --depth 1 https://github.com/ebiggers/libdeflate.git && \
+    cd libdeflate && cmake -B build && cmake --build build && \
+    cp /libdeflate/build/libdeflate.a /usr/local/lib && cp /libdeflate/libdeflate.h /usr/local/include && \
+    cd .. && rm -rf libdeflate
+
+RUN cd / && \
+    wget -q https://nim-lang.org/download/nim-${nim_version}-linux_x64.tar.xz && \
+    tar xf nim-${nim_version}-linux_x64.tar.xz && \
+    echo 'PATH=/nim-${nim_version}/bin:$PATH' >> ~/.bashrc && \
+    echo 'PATH=/nim-${nim_version}/bin:$PATH' >> ~/.bash_profile && \
+    echo 'PATH=/nim-${nim_version}/bin:$PATH' >> /etc/environment  && \
+    rm -f nim-${nim_version}-linux_x64.tar.xz
+
+ENV PATH=/nim-${nim_version}/bin/:$PATH
+
+RUN cd / && \
+    git clone --depth 1 -b 1.15 --recursive https://github.com/samtools/htslib && \
+    cd htslib && autoheader && autoconf && \
+    ./configure --enable-s3 --enable-gcs --enable-libcurl --with-libdeflate && \
+    make -j4 CFLAGS="-fPIC -O3" install && \
+    cd ../ && \
+    git clone --depth 1 -b 1.15 --recursive https://github.com/samtools/bcftools && \
+    cd bcftools && autoheader && autoconf && \
+    ./configure --enable-s3 --enable-libcurl --with-libdeflate && \
+    make -j4 CFLAGS="-fPIC -O3" install && \
+    cd ../ && rm -rf htslib bcftools
+
+RUN cd / &&    \
+    git clone -b v0.2.16 --depth 1 https://github.com/brentp/somalier.git && \
+    cd somalier && \
+    nimble install -y nimble && \
+    /root/.nimble/bin/nimble install -d -y
+
+RUN cd /somalier &&  \
+    nim c -d:danger -d:nsb_static -d:release -d:openmp -d:blas=openblas -d:lapack=openblas -o:/usr/bin/somalier src/somalier && \
+    cp scripts/ancestry-labels-1kg.tsv / && \
+    rm -rf /somalier && somalier --help
+
+ENV somalier_ancestry_labels /ancestry_labels-1kg.tsv
+
+RUN adduser -D defaultuser
+
+USER defaultuser
 

From dabb106caaf281e91925ee3cb8875d31e58beccb Mon Sep 17 00:00:00 2001
From: Vadym <vadym.ivanchuk@scilifelab.se>
Date: Fri, 9 Aug 2024 11:08:08 +0200
Subject: [PATCH 15/38] Clean Dockerfile

---
 BALSAMIC/containers/varcall_py3/Dockerfile | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/BALSAMIC/containers/varcall_py3/Dockerfile b/BALSAMIC/containers/varcall_py3/Dockerfile
index 638bb3a8a..c1ef9e1d6 100644
--- a/BALSAMIC/containers/varcall_py3/Dockerfile
+++ b/BALSAMIC/containers/varcall_py3/Dockerfile
@@ -16,12 +16,14 @@ ARG CONTAINER_NAME
 # Set the working directory
 WORKDIR /project
 
-# Copy all project files to WORKDIR
-COPY . .
+# Copy the relevant container folder into the image
+COPY BALSAMIC/containers/${CONTAINER_NAME}/ /project/BALSAMIC/containers/${CONTAINER_NAME}/
 
-# Execute the container specific script
+# Set the working directory to the container directory
 WORKDIR /project/BALSAMIC/containers/${CONTAINER_NAME}
-RUN /bin/sh ${CONTAINER_NAME}.sh ${CONTAINER_NAME}
+
+# Run the script
+RUN sh ${CONTAINER_NAME}.sh ${CONTAINER_NAME}
 
 # Clean up work environment
 WORKDIR /

From 4e9b268e7c3055104f1a5e1fbe37746d568c26ed Mon Sep 17 00:00:00 2001
From: Vadym <vadym.ivanchuk@scilifelab.se>
Date: Fri, 9 Aug 2024 11:37:12 +0200
Subject: [PATCH 16/38] Minimum version w/o tiddit

---
 .../containers/varcall_py3/varcall_py3.yaml   | 200 ++----------------
 1 file changed, 14 insertions(+), 186 deletions(-)

diff --git a/BALSAMIC/containers/varcall_py3/varcall_py3.yaml b/BALSAMIC/containers/varcall_py3/varcall_py3.yaml
index 05a89fb01..3f329e673 100644
--- a/BALSAMIC/containers/varcall_py3/varcall_py3.yaml
+++ b/BALSAMIC/containers/varcall_py3/varcall_py3.yaml
@@ -5,189 +5,17 @@ channels:
   - defaults
 
 dependencies:
-  - _libgcc_mutex=0.1
-  - _openmp_mutex=4.5
-  - _r-mutex=1.0.1
-  - bcftools=1.15.1
-  - bfc=r181
-  - binutils_impl_linux-64=2.35.1
-  - binutils_linux-64=2.35
-  - brotlipy=0.7.0
-  - bwa=0.7.17
-  - bwidget=1.9.14
-  - bzip2=1.0.8
-  - c-ares=1.18.1
-  - ca-certificates=2022.12.7
-  - cairo=1.16.0
-  - certifi=2022.12.7
-  - cffi=1.14.6
-  - chardet=4.0.0
-  - click=8.0.4
-  - coloredlogs=15.0.1
-  - conda=23.1.0
-  - conda-package-handling=2.0.2
-  - conda-package-streaming=0.7.0
-  - cryptography=39.0.0
-  - curl=7.86.0
-  - cyvcf2=0.30.16
-  - expat=2.5.0
-  - fermi2=r193
-  - font-ttf-dejavu-sans-mono=2.37
-  - font-ttf-inconsolata=3.000
-  - font-ttf-source-code-pro=2.038
-  - font-ttf-ubuntu=0.83
-  - fontconfig=2.14.2
-  - fonts-conda-ecosystem=1
-  - fonts-conda-forge=1
-  - freetype=2.12.1
-  - fribidi=1.0.10
-  - gcc_impl_linux-64=9.3.0
-  - gcc_linux-64=9.3.0
-  - gettext=0.21.1
-  - gfortran_impl_linux-64=9.3.0
-  - gfortran_linux-64=9.3.0
-  - graphite2=1.3.13
-  - gsl=2.7
-  - gxx_impl_linux-64=9.3.0
-  - gxx_linux-64=9.3.0
-  - harfbuzz=3.0.0
-  - htslib=1.15.1
-  - humanfriendly=10.0
-  - icu=68.2
-  - idna=2.10
-  - joblib=1.2.0
-  - jpeg=9e
-  - kernel-headers_linux-64=2.6.32
-  - keyutils=1.6.1
-  - krb5=1.19.3
-  - ld_impl_linux-64=2.35.1
-  - lerc=3.0
-  - libblas=3.9.0
-  - libcblas=3.9.0
-  - libcurl=7.86.0
-  - libdeflate=1.10
-  - libedit=3.1.20191231
-  - libev=4.33
-  - libffi=3.3
-  - libgcc-devel_linux-64=9.3.0
-  - libgcc-ng=12.2.0
-  - libgfortran-ng=9.5.0
-  - libgfortran5=9.5.0
-  - libglib=2.68.4
-  - libgomp=12.2.0
-  - libiconv=1.17
-  - liblapack=3.9.0
-  - libnghttp2=1.51.0
-  - libopenblas=0.3.18
-  - libpng=1.6.39
-  - libssh2=1.10.0
-  - libstdcxx-devel_linux-64=9.3.0
-  - libstdcxx-ng=12.2.0
-  - libtiff=4.4.0
-  - libuuid=2.32.1
-  - libwebp-base=1.2.4
-  - libxcb=1.13
-  - libxml2=2.9.12
-  - libzlib=1.2.13
-  - make=4.3
-  - ncurses=6.3
-  - numpy=1.24.2
-  - openjdk=8.0.332
-  - openssl=1.1.1t
-  - pango=1.48.10
-  - pcre=8.45
-  - pcre2=10.37
-  - perl=5.26.2
-  - pip=23.0.1
-  - pixman=0.40.0
-  - pluggy=1.0.0
-  - pthread-stubs=0.4
-  - pycosat=0.6.4
-  - pycparser=2.20
-  - pyopenssl=20.0.1
-  - pysam=0.19.1
-  - pysocks=1.7.1
-  - python=3.8.12
-  - python_abi=3.8
-  - r-base=4.1.1
-  - r-bitops=1.0_7
-  - r-catools=1.18.2
-  - r-cli=3.6.0
-  - r-colorspace=2.1_0
-  - r-crayon=1.5.2
-  - r-ellipsis=0.3.2
-  - r-fansi=1.0.4
-  - r-farver=2.1.1
-  - r-ggplot2=3.4.1
-  - r-glue=1.6.2
-  - r-gplots=3.1.3
-  - r-gsalib=2.2.1
-  - r-gtable=0.3.1
-  - r-gtools=3.9.4
-  - r-isoband=0.2.7
-  - r-kernsmooth=2.23_20
-  - r-labeling=0.4.2
-  - r-lattice=0.20_45
-  - r-lifecycle=1.0.3
-  - r-magrittr=2.0.3
-  - r-mass=7.3_58.2
-  - r-matrix=1.5_3
-  - r-mgcv=1.8_41
-  - r-munsell=0.5.0
-  - r-nlme=3.1_155
-  - r-pillar=1.8.1
-  - r-pkgconfig=2.0.3
-  - r-plyr=1.8.8
-  - r-r6=2.5.1
-  - r-rcolorbrewer=1.1_3
-  - r-rcpp=1.0.10
-  - r-reshape=0.8.9
-  - r-rlang=1.0.6
-  - r-scales=1.2.1
-  - r-tibble=3.1.8
-  - r-utf8=1.2.3
-  - r-vctrs=0.5.2
-  - r-viridislite=0.4.1
-  - r-withr=2.5.0
-  - readline=8.1.2
-  - requests=2.25.1
-  - ropebwt2=r187
-  - ruamel.yaml=0.17.21
-  - ruamel.yaml.clib=0.2.7
-  - samtools=1.15.1
-  - sed=4.8
-  - seqtk=1.3
-  - setuptools=67.4.0
-  - six=1.16.0
-  - sqlite=3.36.0
-  - svdb=2.8.1
-  - sysroot_linux-64=2.12
-  - tabix=1.11
-  - tiddit=3.7.0
-  - tk=8.6.12
-  - tktable=2.10
-  - toolz=0.12.0
-  - tqdm=4.61.2
-  - tzdata=2021a
-  - urllib3=1.26.6
-  - vardict=2019.06.04
-  - vardict-java=1.8.3
-  - vcfpy=0.13.4
-  - wheel=0.36.2
-  - xorg-kbproto=1.0.7
-  - xorg-libice=1.0.10
-  - xorg-libsm=1.2.3
-  - xorg-libx11=1.7.2
-  - xorg-libxau=1.0.9
-  - xorg-libxdmcp=1.1.3
-  - xorg-libxext=1.3.4
-  - xorg-libxrender=0.9.10
-  - xorg-libxt=1.2.1
-  - xorg-renderproto=0.11.1
-  - xorg-xextproto=7.3.0
-  - xorg-xproto=7.0.31
-  - xz=5.2.5
-  - yaml=0.2.5
-  - zlib=1.2.13
-  - zstandard=0.19.0
-  - zstd=1.5.2
+  - anaconda::python=3.8
+  - anaconda::click=8.0.4
+  - bioconda::bcftools=1.15
+  - bioconda::tabix=1.11
+  - bioconda::samtools=1.15
+  - bioconda::gatk=3.8
+  - bioconda::vardict=2019.06.04
+  - bioconda::vardict-java=1.8.3
+  - bioconda::svdb=2.8.1
+  - bioconda::vcfpy=0.13.4
+  - bioconda::cyvcf2=0.30.16
+  - bioconda::bwa=0.7.17
+  - conda-forge::libiconv
+  - conda-forge::r-base=4.1.1

From db910e758bf2c45d09eae852dab78c7c86f7c806 Mon Sep 17 00:00:00 2001
From: Vadym <vadym.ivanchuk@scilifelab.se>
Date: Fri, 9 Aug 2024 12:57:35 +0200
Subject: [PATCH 17/38] resturcture install

---
 BALSAMIC/containers/varcall_py3/Dockerfile | 14 +++++++++-----
 1 file changed, 9 insertions(+), 5 deletions(-)

diff --git a/BALSAMIC/containers/varcall_py3/Dockerfile b/BALSAMIC/containers/varcall_py3/Dockerfile
index c1ef9e1d6..b0a2b17fe 100644
--- a/BALSAMIC/containers/varcall_py3/Dockerfile
+++ b/BALSAMIC/containers/varcall_py3/Dockerfile
@@ -13,18 +13,22 @@ RUN apk add --no-cache bash gcc git
 
 ARG CONTAINER_NAME
 
-# Set the working directory
-WORKDIR /project
-
-# Copy the relevant container folder into the image
+# Copy the container folder into the image
 COPY BALSAMIC/containers/${CONTAINER_NAME}/ /project/BALSAMIC/containers/${CONTAINER_NAME}/
 
 # Set the working directory to the container directory
 WORKDIR /project/BALSAMIC/containers/${CONTAINER_NAME}
 
-# Run the script
+# Run the package installation script
 RUN sh ${CONTAINER_NAME}.sh ${CONTAINER_NAME}
 
+# Install TIDDIT
+WORKDIR /project
+RUN python -m pip install --upgrade pip
+#RUN git clone --branch v3.8.0 --single-branch https://github.com/TIDDIT/TIDDIT.git && \
+#    cd TIDDIT && \
+#    pip install . \
+
 # Clean up work environment
 WORKDIR /
 RUN rm -rf /project && conda clean --all --yes

From 6a8bf52cc682a0d6d83b27d881bc0f02bc2ffebc Mon Sep 17 00:00:00 2001
From: Vadym <vadym.ivanchuk@scilifelab.se>
Date: Fri, 9 Aug 2024 13:05:24 +0200
Subject: [PATCH 18/38] only build varcall py3

---
 .github/workflows/docker_build_publish_develop.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/docker_build_publish_develop.yml b/.github/workflows/docker_build_publish_develop.yml
index 4e858c8d8..6a9a55f0a 100644
--- a/.github/workflows/docker_build_publish_develop.yml
+++ b/.github/workflows/docker_build_publish_develop.yml
@@ -15,7 +15,7 @@ jobs:
     strategy:
       fail-fast: true
       matrix:
-        container-name: [align_qc, annotate, ascatNgs, cadd, cnvkit, cnvpytor, coverage_qc, delly, gatk, htslib, multiqc, msisensorpro, purecn, varcall_py3, varcall_py27, vcf2cytosure]
+        container-name: [varcall_py3]
     steps:
       - name: Git checkout
         id: git_checkout

From 569646783bab203e42190df3f8affa9481e2e357 Mon Sep 17 00:00:00 2001
From: Vadym <vadym.ivanchuk@scilifelab.se>
Date: Fri, 9 Aug 2024 13:09:09 +0200
Subject: [PATCH 19/38] split rm

---
 BALSAMIC/containers/varcall_py3/Dockerfile | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/BALSAMIC/containers/varcall_py3/Dockerfile b/BALSAMIC/containers/varcall_py3/Dockerfile
index b0a2b17fe..80befd25e 100644
--- a/BALSAMIC/containers/varcall_py3/Dockerfile
+++ b/BALSAMIC/containers/varcall_py3/Dockerfile
@@ -31,4 +31,5 @@ RUN python -m pip install --upgrade pip
 
 # Clean up work environment
 WORKDIR /
-RUN rm -rf /project && conda clean --all --yes
+RUN rm -rf /project
+RUN conda clean --all --yes

From 521c6270851edec2f122a0c1fc816495f39b3bb8 Mon Sep 17 00:00:00 2001
From: Vadym <vadym.ivanchuk@scilifelab.se>
Date: Fri, 9 Aug 2024 13:25:57 +0200
Subject: [PATCH 20/38] Upgrade requests

---
 BALSAMIC/containers/varcall_py3/Dockerfile | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/BALSAMIC/containers/varcall_py3/Dockerfile b/BALSAMIC/containers/varcall_py3/Dockerfile
index 80befd25e..27e4ef791 100644
--- a/BALSAMIC/containers/varcall_py3/Dockerfile
+++ b/BALSAMIC/containers/varcall_py3/Dockerfile
@@ -24,7 +24,8 @@ RUN sh ${CONTAINER_NAME}.sh ${CONTAINER_NAME}
 
 # Install TIDDIT
 WORKDIR /project
-RUN python -m pip install --upgrade pip
+RUN python -m pip install --upgrade pip && \
+    pip install --upgrade requests
 #RUN git clone --branch v3.8.0 --single-branch https://github.com/TIDDIT/TIDDIT.git && \
 #    cd TIDDIT && \
 #    pip install . \

From 1232bafe5f2e00040b6c44e1837b06344bcc88ff Mon Sep 17 00:00:00 2001
From: Vadym <vadym.ivanchuk@scilifelab.se>
Date: Fri, 9 Aug 2024 13:42:30 +0200
Subject: [PATCH 21/38] Install TIDDIT

---
 BALSAMIC/containers/varcall_py3/Dockerfile | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/BALSAMIC/containers/varcall_py3/Dockerfile b/BALSAMIC/containers/varcall_py3/Dockerfile
index 27e4ef791..17089eb43 100644
--- a/BALSAMIC/containers/varcall_py3/Dockerfile
+++ b/BALSAMIC/containers/varcall_py3/Dockerfile
@@ -25,10 +25,10 @@ RUN sh ${CONTAINER_NAME}.sh ${CONTAINER_NAME}
 # Install TIDDIT
 WORKDIR /project
 RUN python -m pip install --upgrade pip && \
-    pip install --upgrade requests
-#RUN git clone --branch v3.8.0 --single-branch https://github.com/TIDDIT/TIDDIT.git && \
-#    cd TIDDIT && \
-#    pip install . \
+    pip install --upgrade requests && \
+    git clone --branch v3.8.0 --single-branch https://github.com/TIDDIT/TIDDIT.git && \
+    cd TIDDIT && \
+    pip install .
 
 # Clean up work environment
 WORKDIR /

From 35a7f00a369ebab125894e4c641024e4c288303a Mon Sep 17 00:00:00 2001
From: Vadym <vadym.ivanchuk@scilifelab.se>
Date: Fri, 9 Aug 2024 13:52:55 +0200
Subject: [PATCH 22/38] link typo

---
 BALSAMIC/containers/varcall_py3/Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/BALSAMIC/containers/varcall_py3/Dockerfile b/BALSAMIC/containers/varcall_py3/Dockerfile
index 17089eb43..b7119f80e 100644
--- a/BALSAMIC/containers/varcall_py3/Dockerfile
+++ b/BALSAMIC/containers/varcall_py3/Dockerfile
@@ -26,7 +26,7 @@ RUN sh ${CONTAINER_NAME}.sh ${CONTAINER_NAME}
 WORKDIR /project
 RUN python -m pip install --upgrade pip && \
     pip install --upgrade requests && \
-    git clone --branch v3.8.0 --single-branch https://github.com/TIDDIT/TIDDIT.git && \
+    git clone --branch v3.8.0 --single-branch https://github.com/SciLifeLab/TIDDIT.git && \
     cd TIDDIT && \
     pip install .
 

From 623f45096208fbd7a753fbe1efcd24adb255cc46 Mon Sep 17 00:00:00 2001
From: Vadym <vadym.ivanchuk@scilifelab.se>
Date: Fri, 9 Aug 2024 14:21:28 +0200
Subject: [PATCH 23/38] weird version

---
 BALSAMIC/containers/varcall_py3/Dockerfile | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/BALSAMIC/containers/varcall_py3/Dockerfile b/BALSAMIC/containers/varcall_py3/Dockerfile
index b7119f80e..a66e7c2dd 100644
--- a/BALSAMIC/containers/varcall_py3/Dockerfile
+++ b/BALSAMIC/containers/varcall_py3/Dockerfile
@@ -24,9 +24,8 @@ RUN sh ${CONTAINER_NAME}.sh ${CONTAINER_NAME}
 
 # Install TIDDIT
 WORKDIR /project
-RUN python -m pip install --upgrade pip && \
-    pip install --upgrade requests && \
-    git clone --branch v3.8.0 --single-branch https://github.com/SciLifeLab/TIDDIT.git && \
+RUN python -m pip install --upgrade pip requests && \
+    git clone --depth 1 --branch TIDDIT-3.8.0 https://github.com/SciLifeLab/TIDDIT.git && \
     cd TIDDIT && \
     pip install .
 

From 27c727c9bf6f7cb1bf279e36a732af4a95fcf8b5 Mon Sep 17 00:00:00 2001
From: Vadym <vadym.ivanchuk@scilifelab.se>
Date: Fri, 9 Aug 2024 14:29:13 +0200
Subject: [PATCH 24/38] multpel rurns

---
 BALSAMIC/containers/varcall_py3/Dockerfile | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/BALSAMIC/containers/varcall_py3/Dockerfile b/BALSAMIC/containers/varcall_py3/Dockerfile
index a66e7c2dd..1c6103e99 100644
--- a/BALSAMIC/containers/varcall_py3/Dockerfile
+++ b/BALSAMIC/containers/varcall_py3/Dockerfile
@@ -31,5 +31,4 @@ RUN python -m pip install --upgrade pip requests && \
 
 # Clean up work environment
 WORKDIR /
-RUN rm -rf /project
-RUN conda clean --all --yes
+RUN rm -rf /project && conda clean --all --yes

From a8aad12356c080c86831cb378d7e14a9d7b89d91 Mon Sep 17 00:00:00 2001
From: Vadym <vadym.ivanchuk@scilifelab.se>
Date: Fri, 9 Aug 2024 14:39:39 +0200
Subject: [PATCH 25/38] en fin...

---
 BALSAMIC/containers/varcall_py3/Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/BALSAMIC/containers/varcall_py3/Dockerfile b/BALSAMIC/containers/varcall_py3/Dockerfile
index 1c6103e99..1589dbc52 100644
--- a/BALSAMIC/containers/varcall_py3/Dockerfile
+++ b/BALSAMIC/containers/varcall_py3/Dockerfile
@@ -24,7 +24,7 @@ RUN sh ${CONTAINER_NAME}.sh ${CONTAINER_NAME}
 
 # Install TIDDIT
 WORKDIR /project
-RUN python -m pip install --upgrade pip requests && \
+RUN python -m pip install --upgrade pip requests pyximport && \
     git clone --depth 1 --branch TIDDIT-3.8.0 https://github.com/SciLifeLab/TIDDIT.git && \
     cd TIDDIT && \
     pip install .

From e81aeac0323f65923da491e3a76ce2894c78ad2d Mon Sep 17 00:00:00 2001
From: Vadym <vadym.ivanchuk@scilifelab.se>
Date: Fri, 9 Aug 2024 15:01:21 +0200
Subject: [PATCH 26/38] cython

---
 BALSAMIC/containers/varcall_py3/Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/BALSAMIC/containers/varcall_py3/Dockerfile b/BALSAMIC/containers/varcall_py3/Dockerfile
index 1589dbc52..f0fc15d4c 100644
--- a/BALSAMIC/containers/varcall_py3/Dockerfile
+++ b/BALSAMIC/containers/varcall_py3/Dockerfile
@@ -24,7 +24,7 @@ RUN sh ${CONTAINER_NAME}.sh ${CONTAINER_NAME}
 
 # Install TIDDIT
 WORKDIR /project
-RUN python -m pip install --upgrade pip requests pyximport && \
+RUN python -m pip install --upgrade pip requests cython && \
     git clone --depth 1 --branch TIDDIT-3.8.0 https://github.com/SciLifeLab/TIDDIT.git && \
     cd TIDDIT && \
     pip install .

From 23e9a75fe2731ef0edfc0d6b46df457b0a261fa3 Mon Sep 17 00:00:00 2001
From: Vadym <vadym.ivanchuk@scilifelab.se>
Date: Fri, 9 Aug 2024 15:12:44 +0200
Subject: [PATCH 27/38] musl dev

---
 BALSAMIC/containers/varcall_py3/Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/BALSAMIC/containers/varcall_py3/Dockerfile b/BALSAMIC/containers/varcall_py3/Dockerfile
index f0fc15d4c..425c36e5a 100644
--- a/BALSAMIC/containers/varcall_py3/Dockerfile
+++ b/BALSAMIC/containers/varcall_py3/Dockerfile
@@ -9,7 +9,7 @@ LABEL base.image="continuumio/miniconda3:4.10.3-alpine" \
 ENV PATH="/opt/conda/bin/:${PATH}"
 
 # Install necessary packages
-RUN apk add --no-cache bash gcc git
+RUN apk add --no-cache bash gcc git musl-dev
 
 ARG CONTAINER_NAME
 

From a22a2fcb91cddcf0144108f14d4f98859d54f7b4 Mon Sep 17 00:00:00 2001
From: Vadym <vadym.ivanchuk@scilifelab.se>
Date: Fri, 9 Aug 2024 15:28:15 +0200
Subject: [PATCH 28/38] removing requests

---
 BALSAMIC/containers/varcall_py3/Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/BALSAMIC/containers/varcall_py3/Dockerfile b/BALSAMIC/containers/varcall_py3/Dockerfile
index 425c36e5a..270c54ac8 100644
--- a/BALSAMIC/containers/varcall_py3/Dockerfile
+++ b/BALSAMIC/containers/varcall_py3/Dockerfile
@@ -24,7 +24,7 @@ RUN sh ${CONTAINER_NAME}.sh ${CONTAINER_NAME}
 
 # Install TIDDIT
 WORKDIR /project
-RUN python -m pip install --upgrade pip requests cython && \
+RUN python -m pip install --upgrade pip cython && \
     git clone --depth 1 --branch TIDDIT-3.8.0 https://github.com/SciLifeLab/TIDDIT.git && \
     cd TIDDIT && \
     pip install .

From e48dd7087f1a642c541442e6f75f08dd82ce6522 Mon Sep 17 00:00:00 2001
From: Vadym <vadym.ivanchuk@scilifelab.se>
Date: Fri, 9 Aug 2024 15:46:31 +0200
Subject: [PATCH 29/38] requests

---
 BALSAMIC/containers/varcall_py3/Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/BALSAMIC/containers/varcall_py3/Dockerfile b/BALSAMIC/containers/varcall_py3/Dockerfile
index 270c54ac8..425c36e5a 100644
--- a/BALSAMIC/containers/varcall_py3/Dockerfile
+++ b/BALSAMIC/containers/varcall_py3/Dockerfile
@@ -24,7 +24,7 @@ RUN sh ${CONTAINER_NAME}.sh ${CONTAINER_NAME}
 
 # Install TIDDIT
 WORKDIR /project
-RUN python -m pip install --upgrade pip cython && \
+RUN python -m pip install --upgrade pip requests cython && \
     git clone --depth 1 --branch TIDDIT-3.8.0 https://github.com/SciLifeLab/TIDDIT.git && \
     cd TIDDIT && \
     pip install .

From 7dbb234da799f48c2683ca834cac72d912c7445c Mon Sep 17 00:00:00 2001
From: Vadym <vadym.ivanchuk@scilifelab.se>
Date: Fri, 9 Aug 2024 15:50:27 +0200
Subject: [PATCH 30/38] ABC

---
 BALSAMIC/containers/varcall_py3/Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/BALSAMIC/containers/varcall_py3/Dockerfile b/BALSAMIC/containers/varcall_py3/Dockerfile
index 425c36e5a..f1fd745fc 100644
--- a/BALSAMIC/containers/varcall_py3/Dockerfile
+++ b/BALSAMIC/containers/varcall_py3/Dockerfile
@@ -24,7 +24,7 @@ RUN sh ${CONTAINER_NAME}.sh ${CONTAINER_NAME}
 
 # Install TIDDIT
 WORKDIR /project
-RUN python -m pip install --upgrade pip requests cython && \
+RUN python -m pip install --upgrade cython pip requests && \
     git clone --depth 1 --branch TIDDIT-3.8.0 https://github.com/SciLifeLab/TIDDIT.git && \
     cd TIDDIT && \
     pip install .

From 04847eb4f520f4f3289d71c70b7d8bcff0b17c4a Mon Sep 17 00:00:00 2001
From: Vadym <vadym.ivanchuk@scilifelab.se>
Date: Fri, 9 Aug 2024 16:11:52 +0200
Subject: [PATCH 31/38] Sonarcloud

---
 BALSAMIC/containers/varcall_py3/Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/BALSAMIC/containers/varcall_py3/Dockerfile b/BALSAMIC/containers/varcall_py3/Dockerfile
index f1fd745fc..b6a2f7edc 100644
--- a/BALSAMIC/containers/varcall_py3/Dockerfile
+++ b/BALSAMIC/containers/varcall_py3/Dockerfile
@@ -24,7 +24,7 @@ RUN sh ${CONTAINER_NAME}.sh ${CONTAINER_NAME}
 
 # Install TIDDIT
 WORKDIR /project
-RUN python -m pip install --upgrade cython pip requests && \
+RUN python -m pip install --no-cache-dir --upgrade cython pip requests && \
     git clone --depth 1 --branch TIDDIT-3.8.0 https://github.com/SciLifeLab/TIDDIT.git && \
     cd TIDDIT && \
     pip install .

From 7ca5529572c76c7361256546246015a63d87236d Mon Sep 17 00:00:00 2001
From: Vadym <vadym.ivanchuk@scilifelab.se>
Date: Mon, 12 Aug 2024 11:28:59 +0200
Subject: [PATCH 32/38] Specific dependencies

---
 .../containers/varcall_py3/varcall_py3.yaml   | 210 ++++++++++++++++--
 1 file changed, 195 insertions(+), 15 deletions(-)

diff --git a/BALSAMIC/containers/varcall_py3/varcall_py3.yaml b/BALSAMIC/containers/varcall_py3/varcall_py3.yaml
index 3f329e673..d7089f19b 100644
--- a/BALSAMIC/containers/varcall_py3/varcall_py3.yaml
+++ b/BALSAMIC/containers/varcall_py3/varcall_py3.yaml
@@ -1,21 +1,201 @@
 channels:
-  - conda-forge
   - anaconda
+  - conda-forge
   - bioconda
   - defaults
 
 dependencies:
-  - anaconda::python=3.8
-  - anaconda::click=8.0.4
-  - bioconda::bcftools=1.15
-  - bioconda::tabix=1.11
-  - bioconda::samtools=1.15
-  - bioconda::gatk=3.8
-  - bioconda::vardict=2019.06.04
-  - bioconda::vardict-java=1.8.3
-  - bioconda::svdb=2.8.1
-  - bioconda::vcfpy=0.13.4
-  - bioconda::cyvcf2=0.30.16
-  - bioconda::bwa=0.7.17
-  - conda-forge::libiconv
-  - conda-forge::r-base=4.1.1
+  - _libgcc_mutex=0.1
+  - _openmp_mutex=4.5
+  - _r-mutex=1.0.1
+  - _sysroot_linux-64_curr_repodata_hack=3
+  - bcftools=1.15.1
+  - binutils_impl_linux-64=2.35.1
+  - binutils_linux-64=2.35
+  - boltons=24.0.0
+  - brotlipy=0.7.0
+  - bwa=0.7.17
+  - bwidget=1.9.14
+  - bzip2=1.0.8
+  - c-ares=1.32.3
+  - ca-certificates=2024.7.4
+  - cairo=1.16.0
+  - certifi=2024.7.4
+  - cffi=1.14.6
+  - chardet=4.0.0
+  - click=8.0.4
+  - coloredlogs=15.0.1
+  - conda=23.7.1
+  - conda-package-handling=2.3.0
+  - conda-package-streaming=0.10.0
+  - cryptography=39.0.0
+  - curl=7.86.0
+  - cyvcf2=0.30.16
+  - expat=2.6.2
+  - font-ttf-dejavu-sans-mono=2.37
+  - font-ttf-inconsolata=3.000
+  - font-ttf-source-code-pro=2.038
+  - font-ttf-ubuntu=0.83
+  - fontconfig=2.14.2
+  - fonts-conda-ecosystem=1
+  - fonts-conda-forge=1
+  - freetype=2.12.1
+  - fribidi=1.0.10
+  - gatk=3.8
+  - gcc_impl_linux-64=9.3.0
+  - gcc_linux-64=9.3.0
+  - gettext=0.22.5
+  - gettext-tools=0.22.5
+  - gfortran_impl_linux-64=9.3.0
+  - gfortran_linux-64=9.3.0
+  - graphite2=1.3.13
+  - gsl=2.7
+  - gxx_impl_linux-64=9.3.0
+  - gxx_linux-64=9.3.0
+  - harfbuzz=3.0.0
+  - htslib=1.15.1
+  - humanfriendly=10.0
+  - icu=68.2
+  - idna=2.10
+  - jpeg=9e
+  - jsonpatch=1.33
+  - jsonpointer=3.0.0
+  - kernel-headers_linux-64=3.10.0
+  - keyutils=1.6.1
+  - krb5=1.19.3
+  - ld_impl_linux-64=2.35.1
+  - lerc=4.0.0
+  - libasprintf=0.22.5
+  - libasprintf-devel=0.22.5
+  - libblas=3.9.0
+  - libcblas=3.9.0
+  - libcurl=7.86.0
+  - libdeflate=1.13
+  - libedit=3.1.20191231
+  - libev=4.33
+  - libexpat=2.6.2
+  - libffi=3.3
+  - libgcc-devel_linux-64=9.3.0
+  - libgcc-ng=14.1.0
+  - libgettextpo=0.22.5
+  - libgettextpo-devel=0.22.5
+  - libgfortran-ng=9.5.0
+  - libgfortran5=9.5.0
+  - libglib=2.68.4
+  - libgomp=14.1.0
+  - libiconv=1.17
+  - liblapack=3.9.0
+  - libnghttp2=1.51.0
+  - libopenblas=0.3.18
+  - libpng=1.6.43
+  - libssh2=1.10.0
+  - libstdcxx-devel_linux-64=9.3.0
+  - libstdcxx-ng=14.1.0
+  - libtiff=4.4.0
+  - libuuid=2.38.1
+  - libwebp-base=1.4.0
+  - libxcb=1.16
+  - libxml2=2.9.12
+  - libzlib=1.2.13
+  - make=4.3
+  - ncurses=6.5
+  - numpy=1.24.4
+  - openjdk=8.0.412
+  - openssl=1.1.1w
+  - packaging=24.1
+  - pango=1.48.10
+  - pcre=8.45
+  - pcre2=10.37
+  - perl=5.26.2
+  - pip=24.2
+  - pixman=0.43.2
+  - pluggy=1.5.0
+  - pthread-stubs=0.4
+  - pycosat=0.6.6
+  - pycparser=2.20
+  - pyopenssl=20.0.1
+  - pysam=0.19.1
+  - pysocks=1.7.1
+  - python=3.8.12
+  - python_abi=3.8
+  - r-base=4.1.1
+  - r-bitops=1.0_7
+  - r-catools=1.18.2
+  - r-cli=3.6.1
+  - r-colorspace=2.1_0
+  - r-crayon=1.5.2
+  - r-ellipsis=0.3.2
+  - r-fansi=1.0.4
+  - r-farver=2.1.1
+  - r-ggplot2=3.4.2
+  - r-glue=1.6.2
+  - r-gplots=3.1.3
+  - r-gsalib=2.2.1
+  - r-gtable=0.3.3
+  - r-gtools=3.9.4
+  - r-isoband=0.2.7
+  - r-kernsmooth=2.23_20
+  - r-labeling=0.4.2
+  - r-lattice=0.21_8
+  - r-lifecycle=1.0.3
+  - r-magrittr=2.0.3
+  - r-mass=7.3_58.3
+  - r-matrix=1.5_4.1
+  - r-mgcv=1.8_42
+  - r-munsell=0.5.0
+  - r-nlme=3.1_155
+  - r-pillar=1.9.0
+  - r-pkgconfig=2.0.3
+  - r-plyr=1.8.8
+  - r-r6=2.5.1
+  - r-rcolorbrewer=1.1_3
+  - r-rcpp=1.0.10
+  - r-reshape=0.8.9
+  - r-rlang=1.1.1
+  - r-scales=1.2.1
+  - r-tibble=3.2.1
+  - r-utf8=1.2.3
+  - r-vctrs=0.6.2
+  - r-viridislite=0.4.1
+  - r-withr=2.5.0
+  - readline=8.1
+  - ruamel.yaml=0.17.40
+  - ruamel.yaml.clib=0.2.8
+  - samtools=1.15.1
+  - sed=4.8
+  - setuptools=72.1.0
+  - six=1.16.0
+  - sqlite=3.36.0
+  - svdb=2.8.1
+  - sysroot_linux-64=2.17
+  - tabix=1.11
+  - tk=8.6.13
+  - tktable=2.10
+  - toolz=0.12.1
+  - tqdm=4.61.2
+  - tzdata=2021a
+  - urllib3=1.26.6
+  - vardict=2019.06.04
+  - vardict-java=1.8.3
+  - vcfpy=0.13.4
+  - wheel=0.36.2
+  - xorg-kbproto=1.0.7
+  - xorg-libice=1.1.1
+  - xorg-libsm=1.2.4
+  - xorg-libx11=1.8.9
+  - xorg-libxau=1.0.11
+  - xorg-libxdmcp=1.1.3
+  - xorg-libxext=1.3.4
+  - xorg-libxrender=0.9.11
+  - xorg-libxt=1.3.0
+  - xorg-renderproto=0.11.1
+  - xorg-xextproto=7.3.0
+  - xorg-xproto=7.0.31
+  - xz=5.2.5
+  - yaml=0.2.5
+  - zlib=1.2.13
+  - zstandard=0.23.0
+  - zstd=1.5.6
+  - pip:
+      - charset-normalizer==3.3.2
+      - requests==2.32.3

From ad799e8ebe27a6481c5d2d22fdb791f3111acf82 Mon Sep 17 00:00:00 2001
From: Vadym <vadym.ivanchuk@scilifelab.se>
Date: Mon, 12 Aug 2024 11:47:24 +0200
Subject: [PATCH 33/38] joblib

---
 BALSAMIC/containers/varcall_py3/Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/BALSAMIC/containers/varcall_py3/Dockerfile b/BALSAMIC/containers/varcall_py3/Dockerfile
index b6a2f7edc..9993378a1 100644
--- a/BALSAMIC/containers/varcall_py3/Dockerfile
+++ b/BALSAMIC/containers/varcall_py3/Dockerfile
@@ -24,7 +24,7 @@ RUN sh ${CONTAINER_NAME}.sh ${CONTAINER_NAME}
 
 # Install TIDDIT
 WORKDIR /project
-RUN python -m pip install --no-cache-dir --upgrade cython pip requests && \
+RUN python -m pip install --no-cache-dir --upgrade cython joblib pip requests && \
     git clone --depth 1 --branch TIDDIT-3.8.0 https://github.com/SciLifeLab/TIDDIT.git && \
     cd TIDDIT && \
     pip install .

From 223993ae61c11ba63c221f529613a06d77832a97 Mon Sep 17 00:00:00 2001
From: Vadym <vadym.ivanchuk@scilifelab.se>
Date: Tue, 13 Aug 2024 16:16:10 +0200
Subject: [PATCH 34/38] ok

---
 BALSAMIC/containers/varcall_py3/Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/BALSAMIC/containers/varcall_py3/Dockerfile b/BALSAMIC/containers/varcall_py3/Dockerfile
index 9993378a1..6ea33b628 100644
--- a/BALSAMIC/containers/varcall_py3/Dockerfile
+++ b/BALSAMIC/containers/varcall_py3/Dockerfile
@@ -9,7 +9,7 @@ LABEL base.image="continuumio/miniconda3:4.10.3-alpine" \
 ENV PATH="/opt/conda/bin/:${PATH}"
 
 # Install necessary packages
-RUN apk add --no-cache bash gcc git musl-dev
+RUN apk add --no-cache bash gcc git libssl-dev musl-dev
 
 ARG CONTAINER_NAME
 

From a40b13bb18b7c3a9f1742e99cc2562e6a6fb60d3 Mon Sep 17 00:00:00 2001
From: Vadym <vadym.ivanchuk@scilifelab.se>
Date: Tue, 13 Aug 2024 16:30:07 +0200
Subject: [PATCH 35/38] typo

---
 BALSAMIC/containers/varcall_py3/Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/BALSAMIC/containers/varcall_py3/Dockerfile b/BALSAMIC/containers/varcall_py3/Dockerfile
index 6ea33b628..6361c5e43 100644
--- a/BALSAMIC/containers/varcall_py3/Dockerfile
+++ b/BALSAMIC/containers/varcall_py3/Dockerfile
@@ -9,7 +9,7 @@ LABEL base.image="continuumio/miniconda3:4.10.3-alpine" \
 ENV PATH="/opt/conda/bin/:${PATH}"
 
 # Install necessary packages
-RUN apk add --no-cache bash gcc git libssl-dev musl-dev
+RUN apk add --no-cache bash gcc git libressl-dev musl-dev
 
 ARG CONTAINER_NAME
 

From 8b9cfbe832e15fa5b7b0d1bec21c41ee9c94994f Mon Sep 17 00:00:00 2001
From: Vadym <vadym.ivanchuk@scilifelab.se>
Date: Tue, 13 Aug 2024 17:04:29 +0200
Subject: [PATCH 36/38] remove dev

---
 BALSAMIC/containers/varcall_py3/Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/BALSAMIC/containers/varcall_py3/Dockerfile b/BALSAMIC/containers/varcall_py3/Dockerfile
index 6361c5e43..4aeb4572e 100644
--- a/BALSAMIC/containers/varcall_py3/Dockerfile
+++ b/BALSAMIC/containers/varcall_py3/Dockerfile
@@ -9,7 +9,7 @@ LABEL base.image="continuumio/miniconda3:4.10.3-alpine" \
 ENV PATH="/opt/conda/bin/:${PATH}"
 
 # Install necessary packages
-RUN apk add --no-cache bash gcc git libressl-dev musl-dev
+RUN apk add --no-cache bash gcc git libressl musl-dev
 
 ARG CONTAINER_NAME
 

From b7941f89104a0ca31bc3304bc1c3c62cc8919482 Mon Sep 17 00:00:00 2001
From: Vadym <vadym.ivanchuk@scilifelab.se>
Date: Tue, 13 Aug 2024 17:12:34 +0200
Subject: [PATCH 37/38] remove libssl

---
 BALSAMIC/containers/varcall_py3/Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/BALSAMIC/containers/varcall_py3/Dockerfile b/BALSAMIC/containers/varcall_py3/Dockerfile
index 4aeb4572e..9993378a1 100644
--- a/BALSAMIC/containers/varcall_py3/Dockerfile
+++ b/BALSAMIC/containers/varcall_py3/Dockerfile
@@ -9,7 +9,7 @@ LABEL base.image="continuumio/miniconda3:4.10.3-alpine" \
 ENV PATH="/opt/conda/bin/:${PATH}"
 
 # Install necessary packages
-RUN apk add --no-cache bash gcc git libressl musl-dev
+RUN apk add --no-cache bash gcc git musl-dev
 
 ARG CONTAINER_NAME
 

From c68d17743b045ac64eed58e7b11d57f0fa2b5b7b Mon Sep 17 00:00:00 2001
From: Vadym <vadym.ivanchuk@scilifelab.se>
Date: Tue, 13 Aug 2024 17:22:13 +0200
Subject: [PATCH 38/38] install bwa fermi

---
 BALSAMIC/containers/varcall_py3/Dockerfile | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/BALSAMIC/containers/varcall_py3/Dockerfile b/BALSAMIC/containers/varcall_py3/Dockerfile
index 9993378a1..b1d0cda53 100644
--- a/BALSAMIC/containers/varcall_py3/Dockerfile
+++ b/BALSAMIC/containers/varcall_py3/Dockerfile
@@ -29,6 +29,18 @@ RUN python -m pip install --no-cache-dir --upgrade cython joblib pip requests &&
     cd TIDDIT && \
     pip install .
 
+# Install fermi2
+WORKDIR /project
+RUN git clone https://github.com/lh3/fermi2.git && \
+    cd fermi2 && \
+    make
+
+# Install bwa (includes ropebwt2)
+WORKDIR /project
+RUN git clone https://github.com/lh3/bwa.git && \
+    cd bwa && \
+    make
+
 # Clean up work environment
 WORKDIR /
 RUN rm -rf /project && conda clean --all --yes