From c46e283eb8c7a0f5076df3c48b6a83116d29857b Mon Sep 17 00:00:00 2001 From: Justin Fear Date: Tue, 21 Mar 2017 12:15:44 -0400 Subject: [PATCH 1/7] Changes requirements to an environment. I think it was confusing to have the requirements.txt containing programs that are not pip installable. I think it is clearer to use an environment.yaml. I changed things over to use a yaml file. --- environment.yaml | 11 +++++++++++ pip-requirements.txt | 0 requirements.txt | 11 ----------- travis-setup.sh | 3 +-- 4 files changed, 12 insertions(+), 13 deletions(-) create mode 100644 environment.yaml delete mode 100644 pip-requirements.txt delete mode 100644 requirements.txt diff --git a/environment.yaml b/environment.yaml new file mode 100644 index 0000000..ed5ff19 --- /dev/null +++ b/environment.yaml @@ -0,0 +1,11 @@ +# only put tools that are needed for tests (e.g., `bowtie-build` is needed to make sure +# that bowtie-index worked), not for the wrappers themselves, which should have +# their own environment.yml files. +dependencies: + - bioconda::bowtie2 ==2.3.0 + - bioconda::gffutils ==0.8.7.1 + - bioconda::hisat2 ==2.0.5 + - bioconda::pytest ==3.0.5 + - bioconda::samtools ==1.4 + - bioconda::snakemake ==3.11.2 + - lcdblib ==0.1 diff --git a/pip-requirements.txt b/pip-requirements.txt deleted file mode 100644 index e69de29..0000000 diff --git a/requirements.txt b/requirements.txt deleted file mode 100644 index 27ab3d0..0000000 --- a/requirements.txt +++ /dev/null @@ -1,11 +0,0 @@ -# only put tools that are needed for tests (e.g., `bowtie-build` is needed to make sure -# that bowtie-index worked), not for the wrappers themselves, which should have -# their own environment.yml files. -bowtie2 ==2.3.0 -gffutils ==0.8.7.1 -hisat2 ==2.0.5 -lcdblib ==0.1 -pysam ==0.9.1.4 -pytest ==3.0.5 -samtools ==1.3.1 -snakemake ==3.10.1 diff --git a/travis-setup.sh b/travis-setup.sh index da31fbe..915733d 100755 --- a/travis-setup.sh +++ b/travis-setup.sh @@ -15,5 +15,4 @@ conda config --add channels bioconda conda config --add channels lcdb conda install -y python=3.5 -conda install -y --file requirements.txt -pip install -r pip-requirements.txt +conda env update -y --file environment.yaml From 7f960b218ad88f23d7ad70f374b33ac1dfb78f8d Mon Sep 17 00:00:00 2001 From: Justin Fear Date: Tue, 21 Mar 2017 12:16:55 -0400 Subject: [PATCH 2/7] Updates samtools version to 1.4 --- wrappers/bowtie2/align/environment.yaml | 2 +- wrappers/hisat2/align/environment.yaml | 2 +- wrappers/samtools/index/environment.yaml | 2 +- wrappers/samtools/sort/environment.yaml | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/wrappers/bowtie2/align/environment.yaml b/wrappers/bowtie2/align/environment.yaml index e1502f8..efc1dca 100644 --- a/wrappers/bowtie2/align/environment.yaml +++ b/wrappers/bowtie2/align/environment.yaml @@ -3,5 +3,5 @@ channels: - lcdb dependencies: - bowtie2 ==2.3.0 - - samtools ==1.3.1 + - samtools ==1.4 - lcdblib ==0.1 diff --git a/wrappers/hisat2/align/environment.yaml b/wrappers/hisat2/align/environment.yaml index 1672920..f5da994 100644 --- a/wrappers/hisat2/align/environment.yaml +++ b/wrappers/hisat2/align/environment.yaml @@ -3,5 +3,5 @@ channels: - lcdb dependencies: - hisat2 ==2.0.5 - - samtools ==1.3.1 + - samtools ==1.4 - lcdblib ==0.1 diff --git a/wrappers/samtools/index/environment.yaml b/wrappers/samtools/index/environment.yaml index 69c397b..4956f4d 100644 --- a/wrappers/samtools/index/environment.yaml +++ b/wrappers/samtools/index/environment.yaml @@ -1,4 +1,4 @@ channels: - bioconda dependencies: - - samtools ==1.3.1 + - samtools ==1.4 diff --git a/wrappers/samtools/sort/environment.yaml b/wrappers/samtools/sort/environment.yaml index 69c397b..4956f4d 100644 --- a/wrappers/samtools/sort/environment.yaml +++ b/wrappers/samtools/sort/environment.yaml @@ -1,4 +1,4 @@ channels: - bioconda dependencies: - - samtools ==1.3.1 + - samtools ==1.4 From c37352e40a2f6dff98c6d8661ca56c1b32d4fc17 Mon Sep 17 00:00:00 2001 From: Justin Fear Date: Tue, 21 Mar 2017 12:17:55 -0400 Subject: [PATCH 3/7] Adds lcdb prefix to lcdblib --- environment.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/environment.yaml b/environment.yaml index ed5ff19..62051dc 100644 --- a/environment.yaml +++ b/environment.yaml @@ -8,4 +8,4 @@ dependencies: - bioconda::pytest ==3.0.5 - bioconda::samtools ==1.4 - bioconda::snakemake ==3.11.2 - - lcdblib ==0.1 + - lcdb::lcdblib ==0.1 From 8dc10efc2995f0730bd0f4478dad60de23705bb9 Mon Sep 17 00:00:00 2001 From: Justin Fear Date: Wed, 22 Mar 2017 14:52:09 -0400 Subject: [PATCH 4/7] updates snakemake and pysam requirements --- environment.yaml | 3 ++- test/test_bowtie2.py | 1 - test/test_hisat2.py | 1 - test/test_kallisto.py | 1 - wrappers/rseqc/bam_stat/environment.yaml | 1 + wrappers/rseqc/geneBody_coverage/environment.yaml | 1 + wrappers/rseqc/infer_experiment/environment.yaml | 1 + wrappers/rseqc/tin/environment.yaml | 1 + 8 files changed, 6 insertions(+), 4 deletions(-) diff --git a/environment.yaml b/environment.yaml index 62051dc..841e2b5 100644 --- a/environment.yaml +++ b/environment.yaml @@ -1,11 +1,12 @@ # only put tools that are needed for tests (e.g., `bowtie-build` is needed to make sure # that bowtie-index worked), not for the wrappers themselves, which should have # their own environment.yml files. +name: lcdb-wrapper-tests dependencies: - bioconda::bowtie2 ==2.3.0 - bioconda::gffutils ==0.8.7.1 - bioconda::hisat2 ==2.0.5 - bioconda::pytest ==3.0.5 - - bioconda::samtools ==1.4 - bioconda::snakemake ==3.11.2 + - bioconda::samtools ==1.4 - lcdb::lcdblib ==0.1 diff --git a/test/test_bowtie2.py b/test/test_bowtie2.py index bdbcb7b..03564f3 100644 --- a/test/test_bowtie2.py +++ b/test/test_bowtie2.py @@ -1,5 +1,4 @@ import pytest -import pysam from snakemake.shell import shell from lcdblib.snakemake import aligners from utils import run, dpath, rm, symlink_in_tempdir diff --git a/test/test_hisat2.py b/test/test_hisat2.py index 38cdd76..cd076f3 100644 --- a/test/test_hisat2.py +++ b/test/test_hisat2.py @@ -1,5 +1,4 @@ import pytest -import pysam from snakemake.shell import shell from lcdblib.snakemake import aligners from utils import run, dpath, rm, symlink_in_tempdir diff --git a/test/test_kallisto.py b/test/test_kallisto.py index 0075b16..d3960d2 100644 --- a/test/test_kallisto.py +++ b/test/test_kallisto.py @@ -1,6 +1,5 @@ import pytest import json -import pysam from snakemake.shell import shell from lcdblib.snakemake import aligners from utils import run, dpath, rm, symlink_in_tempdir diff --git a/wrappers/rseqc/bam_stat/environment.yaml b/wrappers/rseqc/bam_stat/environment.yaml index 89166f4..ac0578f 100644 --- a/wrappers/rseqc/bam_stat/environment.yaml +++ b/wrappers/rseqc/bam_stat/environment.yaml @@ -3,3 +3,4 @@ channels: - r dependencies: - rseqc ==2.6.4 + - pysam ==0.10.0 diff --git a/wrappers/rseqc/geneBody_coverage/environment.yaml b/wrappers/rseqc/geneBody_coverage/environment.yaml index e6a2e7f..7ddc0c9 100644 --- a/wrappers/rseqc/geneBody_coverage/environment.yaml +++ b/wrappers/rseqc/geneBody_coverage/environment.yaml @@ -5,4 +5,5 @@ channels: - conda-forge dependencies: - rseqc ==2.6.4 + - pysam ==0.10.0 - r-essentials ==1.5.1 diff --git a/wrappers/rseqc/infer_experiment/environment.yaml b/wrappers/rseqc/infer_experiment/environment.yaml index 89166f4..ac0578f 100644 --- a/wrappers/rseqc/infer_experiment/environment.yaml +++ b/wrappers/rseqc/infer_experiment/environment.yaml @@ -3,3 +3,4 @@ channels: - r dependencies: - rseqc ==2.6.4 + - pysam ==0.10.0 diff --git a/wrappers/rseqc/tin/environment.yaml b/wrappers/rseqc/tin/environment.yaml index 89166f4..ac0578f 100644 --- a/wrappers/rseqc/tin/environment.yaml +++ b/wrappers/rseqc/tin/environment.yaml @@ -3,3 +3,4 @@ channels: - r dependencies: - rseqc ==2.6.4 + - pysam ==0.10.0 From 56f15c020206be828f3accd401670ee710e84bfc Mon Sep 17 00:00:00 2001 From: Justin Fear Date: Wed, 22 Mar 2017 15:46:04 -0400 Subject: [PATCH 5/7] removes -y from travis. --- travis-setup.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/travis-setup.sh b/travis-setup.sh index 915733d..2c7f2db 100755 --- a/travis-setup.sh +++ b/travis-setup.sh @@ -15,4 +15,4 @@ conda config --add channels bioconda conda config --add channels lcdb conda install -y python=3.5 -conda env update -y --file environment.yaml +conda env update --file environment.yaml From eca4cd54917916d1c5918789147280a9c6e88df8 Mon Sep 17 00:00:00 2001 From: Justin Fear Date: Wed, 22 Mar 2017 15:50:19 -0400 Subject: [PATCH 6/7] removes name from environment. --- environment.yaml | 1 - 1 file changed, 1 deletion(-) diff --git a/environment.yaml b/environment.yaml index 841e2b5..82318a6 100644 --- a/environment.yaml +++ b/environment.yaml @@ -1,7 +1,6 @@ # only put tools that are needed for tests (e.g., `bowtie-build` is needed to make sure # that bowtie-index worked), not for the wrappers themselves, which should have # their own environment.yml files. -name: lcdb-wrapper-tests dependencies: - bioconda::bowtie2 ==2.3.0 - bioconda::gffutils ==0.8.7.1 From 11022faa117994965b7b41062e6ac6d4fcbc0e4e Mon Sep 17 00:00:00 2001 From: Justin Fear Date: Wed, 22 Mar 2017 15:55:11 -0400 Subject: [PATCH 7/7] adds -n root so env update works. --- travis-setup.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/travis-setup.sh b/travis-setup.sh index 2c7f2db..8deb7ca 100755 --- a/travis-setup.sh +++ b/travis-setup.sh @@ -15,4 +15,4 @@ conda config --add channels bioconda conda config --add channels lcdb conda install -y python=3.5 -conda env update --file environment.yaml +conda env update -n root --file environment.yaml