From c3022fd1451de3001040ca24435e8c910b823863 Mon Sep 17 00:00:00 2001 From: Pieter Neerincx Date: Thu, 5 Jan 2023 21:41:44 +0100 Subject: [PATCH 01/15] Added new TrimGalore. --- t/TrimGalore/TrimGalore-0.6.7.eb | 42 ++++++++++++++++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 t/TrimGalore/TrimGalore-0.6.7.eb diff --git a/t/TrimGalore/TrimGalore-0.6.7.eb b/t/TrimGalore/TrimGalore-0.6.7.eb new file mode 100644 index 0000000..6a115fc --- /dev/null +++ b/t/TrimGalore/TrimGalore-0.6.7.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/TrimGalore/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = [ + '49b4622c9f839f8a7037fa2f7de9ab873e4fb702f29c14b4d7f095abf6738f74', # 0.6.7.tar.gz +] + +dependencies = [ + ('Python', '3.10.4'), + ('Java', '11', '', SYSTEM), + ('pigz', '2.7'), + ('Perl', '5.34.1', '-bare'), + ('cutadapt', '3.5'), + ('FastQC', '0.11.9', '-Java-%(javaver)s', SYSTEM), +] + +postinstallcmds = [ + "mkdir %(installdir)s/bin && mv %(installdir)s/%(namelower)s %(installdir)s/bin/%(namelower)s", +] + +fix_perl_shebang_for = ['bin/%(namelower)s'] + +sanity_check_paths = { + 'files': ["bin/trim_galore"], + 'dirs': [], +} + +sanity_check_commands = [('trim_galore', '-v')] + +moduleclass = 'bio' From 72de0b6829180ec53fe0d248579205280fffd187 Mon Sep 17 00:00:00 2001 From: Pieter Neerincx Date: Thu, 5 Jan 2023 21:47:00 +0100 Subject: [PATCH 02/15] Fixed filename bug. --- .../{TrimGalore-0.6.7.eb => TrimGalore-0.6.7-GCCcore-11.3.0.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename t/TrimGalore/{TrimGalore-0.6.7.eb => TrimGalore-0.6.7-GCCcore-11.3.0.eb} (100%) diff --git a/t/TrimGalore/TrimGalore-0.6.7.eb b/t/TrimGalore/TrimGalore-0.6.7-GCCcore-11.3.0.eb similarity index 100% rename from t/TrimGalore/TrimGalore-0.6.7.eb rename to t/TrimGalore/TrimGalore-0.6.7-GCCcore-11.3.0.eb From 544f079dfe956cd4c7dcd305b6322c23b4d3fbc5 Mon Sep 17 00:00:00 2001 From: Pieter Neerincx Date: Thu, 5 Jan 2023 21:59:32 +0100 Subject: [PATCH 03/15] Added missing dep. --- .../python-isal-0.11.1-GCCcore-11.3.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 p/python-isal/python-isal-0.11.1-GCCcore-11.3.0.eb diff --git a/p/python-isal/python-isal-0.11.1-GCCcore-11.3.0.eb b/p/python-isal/python-isal-0.11.1-GCCcore-11.3.0.eb new file mode 100644 index 0000000..42c68ca --- /dev/null +++ b/p/python-isal/python-isal-0.11.1-GCCcore-11.3.0.eb @@ -0,0 +1,34 @@ +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'), + ('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' From 28856cf87bacf1e49912a108a8d3a0906f19aa20 Mon Sep 17 00:00:00 2001 From: Pieter Neerincx Date: Thu, 5 Jan 2023 22:17:16 +0100 Subject: [PATCH 04/15] Trying PythonPlus instead of bare Python dep. --- p/python-isal/python-isal-0.11.1-GCCcore-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/p/python-isal/python-isal-0.11.1-GCCcore-11.3.0.eb b/p/python-isal/python-isal-0.11.1-GCCcore-11.3.0.eb index 42c68ca..27e05d4 100644 --- a/p/python-isal/python-isal-0.11.1-GCCcore-11.3.0.eb +++ b/p/python-isal/python-isal-0.11.1-GCCcore-11.3.0.eb @@ -18,7 +18,7 @@ checksums = ['43d885814f1ee19f5c3a7e9ada3d696fe75f19c0853728fe0ade564bc021a78f'] builddependencies = [('binutils', '2.38')] dependencies = [ - ('Python', '3.10.4'), + ('PythonPlus', '3.10.4', 'v23.01.1'), ('ISA-L', '2.30.0'), ] From b17a22d62395d5d702839c1836cd6a711de36a1e Mon Sep 17 00:00:00 2001 From: Pieter Neerincx Date: Thu, 5 Jan 2023 22:52:20 +0100 Subject: [PATCH 05/15] Trying PythonPlus instead of bare Python dep. --- p/python-isal/python-isal-0.11.1-GCCcore-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/p/python-isal/python-isal-0.11.1-GCCcore-11.3.0.eb b/p/python-isal/python-isal-0.11.1-GCCcore-11.3.0.eb index 27e05d4..89664f9 100644 --- a/p/python-isal/python-isal-0.11.1-GCCcore-11.3.0.eb +++ b/p/python-isal/python-isal-0.11.1-GCCcore-11.3.0.eb @@ -18,7 +18,7 @@ checksums = ['43d885814f1ee19f5c3a7e9ada3d696fe75f19c0853728fe0ade564bc021a78f'] builddependencies = [('binutils', '2.38')] dependencies = [ - ('PythonPlus', '3.10.4', 'v23.01.1'), + ('PythonPlus', '3.10.4', '-v23.01.1'), ('ISA-L', '2.30.0'), ] From 618557147f7278a3a0efb53816e6a41ef6ff804b Mon Sep 17 00:00:00 2001 From: Pieter Neerincx Date: Fri, 6 Jan 2023 10:58:06 +0100 Subject: [PATCH 06/15] Trying PythonPlus instead of bare Python dep. --- p/python-isal/python-isal-0.11.1-GCCcore-11.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/p/python-isal/python-isal-0.11.1-GCCcore-11.3.0.eb b/p/python-isal/python-isal-0.11.1-GCCcore-11.3.0.eb index 89664f9..ba178ff 100644 --- a/p/python-isal/python-isal-0.11.1-GCCcore-11.3.0.eb +++ b/p/python-isal/python-isal-0.11.1-GCCcore-11.3.0.eb @@ -18,6 +18,7 @@ checksums = ['43d885814f1ee19f5c3a7e9ada3d696fe75f19c0853728fe0ade564bc021a78f'] builddependencies = [('binutils', '2.38')] dependencies = [ + ('Python', '3.10.4', '-bare'), ('PythonPlus', '3.10.4', '-v23.01.1'), ('ISA-L', '2.30.0'), ] From d8059e9f3ea4dc3eeff9e86b3fb5ed1c64eb0de5 Mon Sep 17 00:00:00 2001 From: Pieter Neerincx Date: Fri, 6 Jan 2023 12:23:49 +0100 Subject: [PATCH 07/15] Bugfix for cutadapt: use Python bare + PythonPlus. --- c/cutadapt/cutadapt-3.5-GCCcore-11.3.0.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/c/cutadapt/cutadapt-3.5-GCCcore-11.3.0.eb b/c/cutadapt/cutadapt-3.5-GCCcore-11.3.0.eb index 46c3be4..c0614f7 100644 --- a/c/cutadapt/cutadapt-3.5-GCCcore-11.3.0.eb +++ b/c/cutadapt/cutadapt-3.5-GCCcore-11.3.0.eb @@ -13,7 +13,8 @@ builddependencies = [('binutils', '2.38')] dependencies = [ ('pigz', '2.7'), - ('Python', '3.10.4'), + ('Python', '3.10.4', '-bare'), + ('PythonPlus', '%(pyver)s', '-v23.01.1'), ('python-isal', '0.11.1'), ] From 6fa0b78345c48192e936c42ca29f354d125fcc91 Mon Sep 17 00:00:00 2001 From: Pieter Neerincx Date: Fri, 6 Jan 2023 20:23:11 +0100 Subject: [PATCH 08/15] Reverting updates to cutadapt-3.5-GCCcore-11.3.0.eb: giving up on making this work. --- c/cutadapt/cutadapt-3.5-GCCcore-11.3.0.eb | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/c/cutadapt/cutadapt-3.5-GCCcore-11.3.0.eb b/c/cutadapt/cutadapt-3.5-GCCcore-11.3.0.eb index c0614f7..cbef54f 100644 --- a/c/cutadapt/cutadapt-3.5-GCCcore-11.3.0.eb +++ b/c/cutadapt/cutadapt-3.5-GCCcore-11.3.0.eb @@ -13,9 +13,7 @@ builddependencies = [('binutils', '2.38')] dependencies = [ ('pigz', '2.7'), - ('Python', '3.10.4', '-bare'), - ('PythonPlus', '%(pyver)s', '-v23.01.1'), - ('python-isal', '0.11.1'), + ('Python', '3.10.4'), ] use_pip = True From 2931626f4145cca3cfae83a39a11f7754a4c5742 Mon Sep 17 00:00:00 2001 From: Pieter Neerincx Date: Fri, 6 Jan 2023 20:31:03 +0100 Subject: [PATCH 09/15] New attempt at TrimGalore 0.6.7 with dep on newer cutadapt 4.2. --- ...tadapt-4.2-GCCcore-11.3.0-requirements.txt | 4 + ...4.2-GCCcore-11.3.0-requirements_hashed.txt | 93 +++++++++++++++++++ c/cutadapt/cutadapt-4.2-GCCcore-11.3.0.eb | 47 ++++++++++ .../TrimGalore-0.6.7-GCCcore-11.3.0.eb | 3 +- 4 files changed, 145 insertions(+), 2 deletions(-) create mode 100644 c/cutadapt/cutadapt-4.2-GCCcore-11.3.0-requirements.txt create mode 100644 c/cutadapt/cutadapt-4.2-GCCcore-11.3.0-requirements_hashed.txt create mode 100644 c/cutadapt/cutadapt-4.2-GCCcore-11.3.0.eb diff --git a/c/cutadapt/cutadapt-4.2-GCCcore-11.3.0-requirements.txt b/c/cutadapt/cutadapt-4.2-GCCcore-11.3.0-requirements.txt new file mode 100644 index 0000000..4eceea5 --- /dev/null +++ b/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 diff --git a/c/cutadapt/cutadapt-4.2-GCCcore-11.3.0-requirements_hashed.txt b/c/cutadapt/cutadapt-4.2-GCCcore-11.3.0-requirements_hashed.txt new file mode 100644 index 0000000..bbe25c2 --- /dev/null +++ b/c/cutadapt/cutadapt-4.2-GCCcore-11.3.0-requirements_hashed.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 diff --git a/c/cutadapt/cutadapt-4.2-GCCcore-11.3.0.eb b/c/cutadapt/cutadapt-4.2-GCCcore-11.3.0.eb new file mode 100644 index 0000000..1a0f728 --- /dev/null +++ b/c/cutadapt/cutadapt-4.2-GCCcore-11.3.0.eb @@ -0,0 +1,47 @@ +easyblock = 'PythonBundle' + +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'), + ('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 = [''] + +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' diff --git a/t/TrimGalore/TrimGalore-0.6.7-GCCcore-11.3.0.eb b/t/TrimGalore/TrimGalore-0.6.7-GCCcore-11.3.0.eb index 6a115fc..4524e8e 100644 --- a/t/TrimGalore/TrimGalore-0.6.7-GCCcore-11.3.0.eb +++ b/t/TrimGalore/TrimGalore-0.6.7-GCCcore-11.3.0.eb @@ -18,11 +18,10 @@ checksums = [ ] dependencies = [ - ('Python', '3.10.4'), ('Java', '11', '', SYSTEM), ('pigz', '2.7'), ('Perl', '5.34.1', '-bare'), - ('cutadapt', '3.5'), + ('cutadapt', '4.2'), ('FastQC', '0.11.9', '-Java-%(javaver)s', SYSTEM), ] From 0bb539c0849a7c680bf976bcc28c27b1263ed6ba Mon Sep 17 00:00:00 2001 From: Pieter Neerincx Date: Fri, 6 Jan 2023 20:33:15 +0100 Subject: [PATCH 10/15] New attempt at TrimGalore 0.6.7 with dep on newer cutadapt 4.2. --- c/cutadapt/cutadapt-4.2-GCCcore-11.3.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/c/cutadapt/cutadapt-4.2-GCCcore-11.3.0.eb b/c/cutadapt/cutadapt-4.2-GCCcore-11.3.0.eb index 1a0f728..7cd6916 100644 --- a/c/cutadapt/cutadapt-4.2-GCCcore-11.3.0.eb +++ b/c/cutadapt/cutadapt-4.2-GCCcore-11.3.0.eb @@ -1,4 +1,4 @@ -easyblock = 'PythonBundle' +easyblock = 'PythonPackage' name = 'cutadapt' version = '4.2' @@ -21,7 +21,7 @@ dependencies = [ # 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 = [''] +checksums = ['2983895837f2b0ba79cca1ea3aacb25ecf6975f7beabff7375c86fde4eaa6fbf'] pip_ignore_installed = False sanity_pip_check = True From 4e271810f0691073414f91867c87d2ca3a046fac Mon Sep 17 00:00:00 2001 From: Pieter Neerincx Date: Fri, 6 Jan 2023 20:36:28 +0100 Subject: [PATCH 11/15] New attempt at TrimGalore 0.6.7 with dep on newer cutadapt 4.2. --- ...ed.txt => cutadapt-4.2-GCCcore-11.3.0-requirements_hashes.txt} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename c/cutadapt/{cutadapt-4.2-GCCcore-11.3.0-requirements_hashed.txt => cutadapt-4.2-GCCcore-11.3.0-requirements_hashes.txt} (100%) diff --git a/c/cutadapt/cutadapt-4.2-GCCcore-11.3.0-requirements_hashed.txt b/c/cutadapt/cutadapt-4.2-GCCcore-11.3.0-requirements_hashes.txt similarity index 100% rename from c/cutadapt/cutadapt-4.2-GCCcore-11.3.0-requirements_hashed.txt rename to c/cutadapt/cutadapt-4.2-GCCcore-11.3.0-requirements_hashes.txt From 8db2a92893038a8c4a854c90c46b188d5307f7ae Mon Sep 17 00:00:00 2001 From: Pieter Neerincx Date: Fri, 6 Jan 2023 20:42:51 +0100 Subject: [PATCH 12/15] Fixed issue due to different executable name. --- t/TrimGalore/TrimGalore-0.6.7-GCCcore-11.3.0.eb | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/t/TrimGalore/TrimGalore-0.6.7-GCCcore-11.3.0.eb b/t/TrimGalore/TrimGalore-0.6.7-GCCcore-11.3.0.eb index 4524e8e..92c86b4 100644 --- a/t/TrimGalore/TrimGalore-0.6.7-GCCcore-11.3.0.eb +++ b/t/TrimGalore/TrimGalore-0.6.7-GCCcore-11.3.0.eb @@ -3,6 +3,8 @@ easyblock = 'Tarball' name = 'TrimGalore' version = '0.6.7' +_local_executable = 'trim_galore' + 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 @@ -26,16 +28,16 @@ dependencies = [ ] postinstallcmds = [ - "mkdir %(installdir)s/bin && mv %(installdir)s/%(namelower)s %(installdir)s/bin/%(namelower)s", + "mkdir %(installdir)s/bin && mv %(installdir)s/%(_local_executable)s %(installdir)s/bin/%(_local_executable)s", ] -fix_perl_shebang_for = ['bin/%(namelower)s'] +fix_perl_shebang_for = ['bin/%(_local_executable)s'] sanity_check_paths = { - 'files': ["bin/trim_galore"], + 'files': ["bin/%(_local_executable)s"], 'dirs': [], } -sanity_check_commands = [('trim_galore', '-v')] +sanity_check_commands = [('%(_local_executable)s', '-v')] moduleclass = 'bio' From a9df294efe81261f6a7c7d689dede5c816598af7 Mon Sep 17 00:00:00 2001 From: Pieter Neerincx Date: Fri, 6 Jan 2023 20:51:26 +0100 Subject: [PATCH 13/15] Fixed issue due to different executable name. --- t/TrimGalore/TrimGalore-0.6.7-GCCcore-11.3.0.eb | 13 ++++++------- 1 file changed, 6 insertions(+), 7 deletions(-) diff --git a/t/TrimGalore/TrimGalore-0.6.7-GCCcore-11.3.0.eb b/t/TrimGalore/TrimGalore-0.6.7-GCCcore-11.3.0.eb index 92c86b4..33ef68e 100644 --- a/t/TrimGalore/TrimGalore-0.6.7-GCCcore-11.3.0.eb +++ b/t/TrimGalore/TrimGalore-0.6.7-GCCcore-11.3.0.eb @@ -3,8 +3,6 @@ easyblock = 'Tarball' name = 'TrimGalore' version = '0.6.7' -_local_executable = 'trim_galore' - 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 @@ -13,7 +11,7 @@ methylation positions for RRBS sequence files (for directional, non-directional toolchain = {'name': 'GCCcore', 'version': '11.3.0'} -source_urls = ['https://github.com/FelixKrueger/TrimGalore/archive/'] +source_urls = ['https://github.com/FelixKrueger/%(name)s/archive/'] sources = ['%(version)s.tar.gz'] checksums = [ '49b4622c9f839f8a7037fa2f7de9ab873e4fb702f29c14b4d7f095abf6738f74', # 0.6.7.tar.gz @@ -28,16 +26,17 @@ dependencies = [ ] postinstallcmds = [ - "mkdir %(installdir)s/bin && mv %(installdir)s/%(_local_executable)s %(installdir)s/bin/%(_local_executable)s", + 'mkdir "%(installdir)s/bin"', + 'mv -v "%(installdir)s/trim_galore" "%(installdir)s/bin/trim_galore"', ] -fix_perl_shebang_for = ['bin/%(_local_executable)s'] +fix_perl_shebang_for = ['bin/trim_galore'] sanity_check_paths = { - 'files': ["bin/%(_local_executable)s"], + 'files': ["bin/trim_galore"], 'dirs': [], } -sanity_check_commands = [('%(_local_executable)s', '-v')] +sanity_check_commands = [('trim_galore', '-v')] moduleclass = 'bio' From 8738f1ddb75ecb3818cf56f15c3438c264af5517 Mon Sep 17 00:00:00 2001 From: Pieter Neerincx Date: Fri, 6 Jan 2023 20:55:53 +0100 Subject: [PATCH 14/15] Reverted another change in cutadapt-3.5-GCCcore-11.3.0.eb --- c/cutadapt/cutadapt-3.5-GCCcore-11.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/c/cutadapt/cutadapt-3.5-GCCcore-11.3.0.eb b/c/cutadapt/cutadapt-3.5-GCCcore-11.3.0.eb index cbef54f..46c3be4 100644 --- a/c/cutadapt/cutadapt-3.5-GCCcore-11.3.0.eb +++ b/c/cutadapt/cutadapt-3.5-GCCcore-11.3.0.eb @@ -14,6 +14,7 @@ builddependencies = [('binutils', '2.38')] dependencies = [ ('pigz', '2.7'), ('Python', '3.10.4'), + ('python-isal', '0.11.1'), ] use_pip = True From bb9b69bf5af5998a91a5700ab03fdb81c7d66acc Mon Sep 17 00:00:00 2001 From: Pieter Neerincx Date: Fri, 6 Jan 2023 21:01:33 +0100 Subject: [PATCH 15/15] Added missing dep. --- c/cutadapt/cutadapt-4.2-GCCcore-11.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/c/cutadapt/cutadapt-4.2-GCCcore-11.3.0.eb b/c/cutadapt/cutadapt-4.2-GCCcore-11.3.0.eb index 7cd6916..e7f108b 100644 --- a/c/cutadapt/cutadapt-4.2-GCCcore-11.3.0.eb +++ b/c/cutadapt/cutadapt-4.2-GCCcore-11.3.0.eb @@ -13,6 +13,7 @@ builddependencies = [('binutils', '2.38')] dependencies = [ ('pigz', '2.7'), + ('ISA-L', '2.30.0'), ('Python', '3.10.4', '-bare'), ]