Merge pull request #17 from pneerincx/trimgalore

Trimgalore

c/cutadapt/cutadapt-4.2-GCCcore-11.3.0-requirements.txt

@@ -0,0 +1,4 @@
+cutadapt==4.2
+dnaio==0.10.0
+isal==1.1.0
+xopen==1.7.0

c/cutadapt/cutadapt-4.2-GCCcore-11.3.0-requirements_hashes.txt

@@ -0,0 +1,93 @@
+#
+# This file is autogenerated by pip-compile with Python 3.10
+# by the following command:
+#
+#    pip-compile --generate-hashes --output-file=requirements_hashed.txt --resolver=backtracking cutadapt-4.2-GCCcore-11.3.0-requirements.txt
+#
+cutadapt==4.2 \
+    --hash=sha256:0b06a2428ca7c133b836b117633940b4c4866fe88b9b844b815d5cf717fb1311 \
+    --hash=sha256:0ed2c81ba0895e62ec5c1d48f53cb1a7863325ba136eb77bf43ca22c610c4df1 \
+    --hash=sha256:66e5f9ea068a65b288c361a3dc416dc73e976ea9a034f4530448fc93b93906cd \
+    --hash=sha256:682696a2759a229f7d8285ac584648b6e3b4eedf4dc161d214aa45cc82ea48b9 \
+    --hash=sha256:79045e114fd24711326020fde9dde802b9309eadab6865d14e00793e31d9564a \
+    --hash=sha256:7a0e041c4704f254a30a094a241b246b4a756f536d9e67f7478a6385b342af7f \
+    --hash=sha256:9768884ef4aeff32cb70cc3a1db0513f589619ab905c46575d9973be772df350 \
+    --hash=sha256:ab0ac450baecc1576cc5ccbc06eab2685be9ee7676763938237d954a644237f1 \
+    --hash=sha256:d69f26c3008a10fba27d5618600decf749bdff6096c850ec3b2efa77e0a2ba34 \
+    --hash=sha256:ef7617329ffa78e5357db355d92671840be2d6d781efbf949e7da54b2de0e4ea \
+    --hash=sha256:fa8514cc9a0c15e8dd06bbfce446b437f75549bfdd94120682aa135b2439899c
+    # via -r cutadapt-4.2-GCCcore-11.3.0-requirements.txt
+dnaio==0.10.0 \
+    --hash=sha256:044c1170ee5a5680c7932e28b9b4b0bc21c481b1a7ef1ce016ece772b321ebe7 \
+    --hash=sha256:1448d222cb942ff28b8e99ee1c615204be160be3db395aa5f4ca19ab4cca496f \
+    --hash=sha256:47232242cf8ddb7df3da26006b22fc28ff87e08d8b36f4f84dc1e2a60bb6f354 \
+    --hash=sha256:5b11e0dec5195db7206a1a5bb1adfa31054757bb5354c90e933c43753edd05be \
+    --hash=sha256:630d7f5cd07a3536deb5d31d3f03c9acfab609d211cd5c51d9ab8e046fa2f805 \
+    --hash=sha256:7b980099c591f870c224ee5158641b8ed65853eb01e4dac7d84f58f1c567623f \
+    --hash=sha256:93e46cb77b0012af380824f9f6b274425afa52b588c699fbb75dbb3a7ebcf94c \
+    --hash=sha256:9c1dea14ce39268f4f7b958fac402d7e6387e6594b68a8283f8f82a37c104104 \
+    --hash=sha256:a2cd08f600bded04fbe35eeb18345d5a1be2a830a3c655f136739ee11adfe82c \
+    --hash=sha256:aa38e2215a2774929207f7a8da906fdd831d468a555e635b6ec570f2acf2e82d \
+    --hash=sha256:baf3a9be3b14a444c51011711365234efa26d2e57574579c0f46e6a61bbed84c \
+    --hash=sha256:dd10fb44dd23829c006dd4d9201b4c7fff7e06b617655f9b453155dbb85f5058 \
+    --hash=sha256:de51a50948f00b864297d74eddb588fbee5ac229855754e77564d18b24619d18 \
+    --hash=sha256:eb75552d373669ca205b2f98d374f960a448da59eeb8f6977c57df52924c2caf \
+    --hash=sha256:f9dc2171e777e3d35391fdcd09e92bdaa121cb7fe426c50633372da1bef93961 \
+    --hash=sha256:f9ff5cd7166b5d8c260c24c4f8e922e6e04c77310b743705072fb2d543c31314
+    # via
+    #   -r cutadapt-4.2-GCCcore-11.3.0-requirements.txt
+    #   cutadapt
+isal==1.1.0 \
+    --hash=sha256:03667ba285b58be34b6eb62115162809f7fc681202e03f35bf64ee3af03f7f36 \
+    --hash=sha256:115503ac706ee5c42bdf760d362013838f4254a64638933842759202abd5855a \
+    --hash=sha256:1364f4e3255a57d51c01422ab3ae785a43c076d516ebf49f6a25adecf8232105 \
+    --hash=sha256:139281e9e7b108bdc4c257f024def2f76dcbf58ccc5958c982c465c4644f8294 \
+    --hash=sha256:1fbca6a7ac71e1b2cc8901eff32868bc7cadb6edd8ed7c3cbe163a67ff1cb435 \
+    --hash=sha256:2a17874d46ed71b1a7f76b5388232fc1e1af7f78664e86bf985db37892848fa8 \
+    --hash=sha256:34b2a0139492df5de8f44dd474948e3c987721dd8fb3f8c2fc935af6389f4de7 \
+    --hash=sha256:3a49605ab48327395d982baf8c12041edf6b266114e91366b70c93b1966b0105 \
+    --hash=sha256:3f3bd81ab5b15af7b55c2ac36ff15077d3799e56760096aff46db9ab49d4e986 \
+    --hash=sha256:41df368a1e9ae63e9f587dd124572704aee0a046df9be192702e8036cf684b5f \
+    --hash=sha256:43cf47e2bbf90237a9a0a0a2b38a0fe3ef4fc8f60483a7b4fe559463f93f967d \
+    --hash=sha256:45a40535c0c3285c66cf686aab58518705c728f8aeb27a512a42efe18bea0f89 \
+    --hash=sha256:4f054a648e8389f3ff208dbcbc1a399b48980d45e03ce1df52a50c418f2ac0dc \
+    --hash=sha256:4ff1a35488e166f978e44a94262cbda56ae86e385be1d5ebce225450cc882785 \
+    --hash=sha256:53ea97dfd273e5af96b92d4ac592d0d325c07c5075ad10fa983e6c4e603652a9 \
+    --hash=sha256:571af022daee2f3d12ff30ae0375a32fe578a70ffde2a28ad1f567983057f9c5 \
+    --hash=sha256:583baa0308997f83225edbf8b6ba48ff217f5d26486c44f7ac695c9e04fc2ed0 \
+    --hash=sha256:59146ce32c146b215eaf567f9f5fe142613ab63fca454d1060ba713ece77b3a4 \
+    --hash=sha256:5af9e10c6e8cb05d11f15b73e3ad8b475a4e488cf0d7323af7d989a02ef35d4c \
+    --hash=sha256:7afda28564ecd9d58d418ff870a0181ce9941fbe92b71ee79ba07db26a5e784d \
+    --hash=sha256:815d6f13091681d79428f87e4a9300226f7d703698b2a1badee2ffb827ad09e0 \
+    --hash=sha256:8322438878ad02fa213f22f54f9b636b0fb8be76de72e69bef3eaf0251d75658 \
+    --hash=sha256:8901922f21136746375df791c32c50019fe591fda728123987d6308e46531e6b \
+    --hash=sha256:90e8c68d3f372071dfb29c607dd6a322ff0198b360d72702747565fad0e2e529 \
+    --hash=sha256:91108e08b81670d5138d6eba12474fe0351f76381d703d22943b490450c6a746 \
+    --hash=sha256:96d20c9bb6d4d0ec399f8cf60ba1d6e656949dd29ad2bda765b1efb638470d8b \
+    --hash=sha256:9a25433c9c2cb6bfd0739506c3ccfdd629d755988ceb75c1ca9730091df17974 \
+    --hash=sha256:9ca8c6f3b8f75f5eea97036d43fb2c3c4eac5a70001500eb5fa67a8ac0fdc830 \
+    --hash=sha256:a31c66e04083326f25b63c0a792590999d34032eb8b1be30b4499e0f7246646e \
+    --hash=sha256:a7edce3d867025338e96ae97a9c8608b383f87ee77e36ae90db1f32378a4a96e \
+    --hash=sha256:b07a2363520af1d94af94cbf4c362f3be3d0bfd0f07623939a4f3521d289f125 \
+    --hash=sha256:b55090be927c742a0f59096925f61b0fde7a010d4ac7ab955addfe27008ea116 \
+    --hash=sha256:bb25cb61fb52fc0cc390140539f8093f3266eef1eaa079f116780f9f9f62c075 \
+    --hash=sha256:d1aaf7c3227ba1cd25eb1dc4e22583ca5442e92f9b917a6055678f61c134322c \
+    --hash=sha256:d1e890ed8fc3f56e1727af0e4e4b24ca87fc92b07eac663d183e76126ecaf87c \
+    --hash=sha256:d4da884ab6fb5cab7b505f35f1e0991a63f4bf76c9e7e627b17a6e26416189de \
+    --hash=sha256:e016bc4b919c069e082c27ec292e707b020a42779a8b878a83153b85df801c16 \
+    --hash=sha256:e4ffed7d9c377fe65fa4f5fa5811a2f61dc573c02c0bbdbbe392bca7ed4bb1a4 \
+    --hash=sha256:ea71f29520e8a729ff081c2ea4e4e051fdd474b5fd06e2d0f783f0ba0d05cdf1 \
+    --hash=sha256:eabfde269c0fbdc4d6e4ffae561ac6abb319d5ba294a08d6fdfda589d3412b0f \
+    --hash=sha256:f314e990a3ab144878cab7994d5702a383c9659adfb5bc2af40a0142fd880e5c \
+    --hash=sha256:f925462741c18a6011b8740f27eab8d6011c7bdf23299bcf34d8d2ab5f0fe3d6 \
+    --hash=sha256:ffebfe58927ef153a2c29e1fd03f9df7b4ca607ec243bcf954f078e2c84efa21
+    # via
+    #   -r cutadapt-4.2-GCCcore-11.3.0-requirements.txt
+    #   xopen
+xopen==1.7.0 \
+    --hash=sha256:901f9c8298e95ed74767a4bd76d9f4cf71d8de27b8cf296ac3e7bc1c11520d9f \
+    --hash=sha256:c4c6c978bb5f6f2a4364438da09f4f8fde078b6df4de18e3f72fccc472d1ee33
+    # via
+    #   -r cutadapt-4.2-GCCcore-11.3.0-requirements.txt
+    #   cutadapt
+    #   dnaio

c/cutadapt/cutadapt-4.2-GCCcore-11.3.0.eb

@@ -0,0 +1,48 @@
+easyblock = 'PythonPackage'
+
+name = 'cutadapt'
+version = '4.2'
+
+homepage = 'https://opensource.scilifelab.se/projects/cutadapt/'
+description = """Cutadapt finds and removes adapter sequences, primers, poly-A tails and
+ other types of unwanted sequence from your high-throughput sequencing reads."""
+
+toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
+
+builddependencies = [('binutils', '2.38')]
+
+dependencies = [
+    ('pigz', '2.7'),
+    ('ISA-L', '2.30.0'),
+    ('Python', '3.10.4', '-bare'),
+]
+
+#
+# Make sure the package list in *requirements_hashes.txt does not contain pip nor setuptools
+# as these packages are already included in the Python "bare" module.
+#
+sources = ['%(name)s-%(version)s-%(toolchain_name)s-%(toolchain_version)s-requirements_hashes.txt']
+checksums = ['2983895837f2b0ba79cca1ea3aacb25ecf6975f7beabff7375c86fde4eaa6fbf']
+
+pip_ignore_installed = False
+sanity_pip_check = True
+unpack_sources = False
+use_pip = True
+use_pip_for_deps = True
+use_pip_requirement = True
+installopts = '--require-hashes'
+
+#
+# Sanity checking.
+#
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['lib/python%(pyshortver)s/site-packages']
+}
+
+sanity_check_commands = [
+    "cutadapt --help",
+    "cutadapt --version",
+]
+
+moduleclass = 'bio'

p/python-isal/python-isal-0.11.1-GCCcore-11.3.0.eb

@@ -0,0 +1,35 @@
+easyblock = 'PythonPackage'
+
+name = 'python-isal'
+version = '0.11.1'
+
+homepage = 'https://github.com/pycompression/python-isal'
+description = """Faster zlib and gzip compatible compression and decompression
+ by providing python bindings for the isa-l library.
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
+
+github_account = 'pycompression'
+source_urls = [GITHUB_SOURCE]
+sources = ['v%(version)s.tar.gz']
+checksums = ['43d885814f1ee19f5c3a7e9ada3d696fe75f19c0853728fe0ade564bc021a78f']
+
+builddependencies = [('binutils', '2.38')]
+
+dependencies = [
+    ('Python', '3.10.4', '-bare'),
+    ('PythonPlus', '3.10.4', '-v23.01.1'),
+    ('ISA-L', '2.30.0'),
+]
+
+use_pip = True
+download_dep_fail = True
+sanity_pip_check = True
+
+preinstallopts = 'PYTHON_ISAL_LINK_DYNAMIC=true'
+installopts = '--no-binary isal'
+
+options = {'modulename': 'isal'}
+
+moduleclass = 'lib'

t/TrimGalore/TrimGalore-0.6.7-GCCcore-11.3.0.eb

@@ -0,0 +1,42 @@
+easyblock = 'Tarball'
+
+name = 'TrimGalore'
+version = '0.6.7'
+
+homepage = 'https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/'
+description = """Trim Galore! is a wrapper script to automate quality and adapter
+trimming as well as quality control, with some added functionality to remove biased
+methylation positions for RRBS sequence files (for directional, non-directional 
+(or paired-end) sequencing)."""
+
+toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
+
+source_urls = ['https://github.com/FelixKrueger/%(name)s/archive/']
+sources = ['%(version)s.tar.gz']
+checksums = [
+    '49b4622c9f839f8a7037fa2f7de9ab873e4fb702f29c14b4d7f095abf6738f74',  # 0.6.7.tar.gz
+]
+
+dependencies = [
+    ('Java', '11', '', SYSTEM),
+    ('pigz', '2.7'),
+    ('Perl', '5.34.1', '-bare'),
+    ('cutadapt', '4.2'),
+    ('FastQC', '0.11.9', '-Java-%(javaver)s', SYSTEM),
+]
+
+postinstallcmds = [
+    'mkdir "%(installdir)s/bin"',
+    'mv -v "%(installdir)s/trim_galore" "%(installdir)s/bin/trim_galore"',
+]
+
+fix_perl_shebang_for = ['bin/trim_galore']
+
+sanity_check_paths = {
+    'files': ["bin/trim_galore"],
+    'dirs': [],
+}
+
+sanity_check_commands = [('trim_galore', '-v')]
+
+moduleclass = 'bio'