From 1495c73a2bf938395b8fca4ad532ee885b15a506 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Thu, 1 Feb 2024 17:56:37 +0100 Subject: [PATCH] #271 cleanup dir --- 271_phyluce/snakemake.eb | 90 ------------------- .../Cbc-2.10.11-foss-2023a.eb | 0 .../Cgl-0.60.8-foss-2023a.eb | 0 .../Clp-1.17.9-foss-2023a.eb | 0 .../CoinUtils-2.11.10-GCC-12.3.0.eb | 0 .../Osi-0.108.9-GCC-12.3.0.eb | 0 .../PuLP-2.8.0-foss-2023a.eb | 0 71_GRASP_suite/GRASPsuite-other-jar.eb | 39 ++++++++ 8 files changed, 39 insertions(+), 90 deletions(-) delete mode 100644 271_phyluce/snakemake.eb rename 271_phyluce/{ => unused_econfigs}/Cbc-2.10.11-foss-2023a.eb (100%) rename 271_phyluce/{ => unused_econfigs}/Cgl-0.60.8-foss-2023a.eb (100%) rename 271_phyluce/{ => unused_econfigs}/Clp-1.17.9-foss-2023a.eb (100%) rename 271_phyluce/{ => unused_econfigs}/CoinUtils-2.11.10-GCC-12.3.0.eb (100%) rename 271_phyluce/{ => unused_econfigs}/Osi-0.108.9-GCC-12.3.0.eb (100%) rename 271_phyluce/{ => unused_econfigs}/PuLP-2.8.0-foss-2023a.eb (100%) create mode 100644 71_GRASP_suite/GRASPsuite-other-jar.eb diff --git a/271_phyluce/snakemake.eb b/271_phyluce/snakemake.eb deleted file mode 100644 index 4025ce5c..00000000 --- a/271_phyluce/snakemake.eb +++ /dev/null @@ -1,90 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'snakemake' -version = '8.2.4' - -homepage = 'https://snakemake.readthedocs.io' -description = "The Snakemake workflow management system is a tool to create reproducible and scalable data analyses." - -toolchain = {'name': 'foss', 'version': '2023a'} - -dependencies = [ #ALL deps are ok - ('Python', '3.11.3'), - ('SciPy-bundle', '2023.07'), - ('GitPython', '3.1.40'), - ('IPython', '8.14.0'), - ('PyYAML', '6.0'), - ('wrapt', '1.15.0'), - ('PuLP', '2.8.0'), -] - -use_pip = True -sanity_pip_check = True - -exts_list = [ #TODO: update exts - ('ConfigArgParse', '1.7', { - 'checksums': ['e7067471884de5478c58a511e529f0f9bd1c66bfef1dea90935438d6c23306d1'], - }), - ('datrie', '0.8.2', { - 'checksums': ['525b08f638d5cf6115df6ccd818e5a01298cd230b2dac91c8ff2e6499d18765d'], - }), - ('toposort', '1.10', { - 'checksums': ['bfbb479c53d0a696ea7402601f4e693c97b0367837c8898bc6471adfca37a6bd'], - }), - ('amply', '0.1.6', { - 'checksums': ['61421103ccf8e1066717115fe7917610d831d551c68d31a110876a5b6c78aea4'], - }), - ('smart-open', '6.3.0', { - 'sources': ['smart_open-%(version)s.tar.gz'], - 'checksums': ['d5238825fe9a9340645fac3d75b287c08fbb99fb2b422477de781c9f5f09e019'], - }), - ('connection-pool', '0.0.3', { - 'sources': ['connection_pool-%(version)s.tar.gz'], - 'checksums': ['bf429e7aef65921c69b4ed48f3d48d3eac1383b05d2df91884705842d974d0dc'], - }), - ('stopit', '1.1.2', { - 'checksums': ['f7f39c583fd92027bd9d06127b259aee7a5b7945c1f1fa56263811e1e766996d'], - }), - ('reretry', '0.11.8', { - 'checksums': ['f2791fcebe512ea2f1d153a2874778523a8064860b591cd90afc21a8bed432e3'], - }), - ('throttler', '1.2.2', { - 'checksums': ['d54db406d98e1b54d18a9ba2b31ab9f093ac64a0a59d730c1cf7bb1cdfc94a58'], - }), - ('dpath', '2.1.6', { - 'checksums': ['f1e07c72e8605c6a9e80b64bc8f42714de08a789c7de417e49c3f87a19692e47'], - }), - ('plac', '1.3.5', { - 'checksums': ['38bdd864d0450fb748193aa817b9c458a8f5319fbf97b2261151cfc0a5812090'], - }), - ('yte', '1.5.1', { - 'checksums': ['6d0b315b78af83276d78f5f67c107c84238f772a76d74f4fc77905b46f3731f5'], - }), - ('humanfriendly', '10.0', { - 'checksums': ['6b0b831ce8f15f7300721aa49829fc4e83921a9a301cc7f606be6686a2288ddc'], - }), - ('nbformat', '5.9.2', { - 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', - 'checksums': ['1c5172d786a41b82bcfd0c23f9e6b6f072e8fb49c39250219e4acfff1efe89e9'], - }), - ('jupyter-core', '5.3.1', { - 'modulename': 'jupyter_core', - 'source_tmpl': 'jupyter_core-%(version)s.tar.gz', - 'checksums': ['5ba5c7938a7f97a6b0481463f7ff0dbac7c15ba48cf46fa4035ca6e838aa1aba'], - }), - ('fastjsonschema', '2.18.0', { - 'checksums': ['e820349dd16f806e4bd1467a138dced9def4bc7d6213a34295272a6cac95b5bd'], - }), - (name, version, { - 'checksums': ['cbe586fe28349982307f008ca40e839d569cf5d540008b0c91ebfef689b49b18'], - }), -] - -sanity_check_paths = { - 'files': ['bin/snakemake'], - 'dirs': ['lib/python%(pyshortver)s/site-packages/snakemake'], -} - -sanity_check_commands = ['snakemake --help'] - -moduleclass = 'tools' diff --git a/271_phyluce/Cbc-2.10.11-foss-2023a.eb b/271_phyluce/unused_econfigs/Cbc-2.10.11-foss-2023a.eb similarity index 100% rename from 271_phyluce/Cbc-2.10.11-foss-2023a.eb rename to 271_phyluce/unused_econfigs/Cbc-2.10.11-foss-2023a.eb diff --git a/271_phyluce/Cgl-0.60.8-foss-2023a.eb b/271_phyluce/unused_econfigs/Cgl-0.60.8-foss-2023a.eb similarity index 100% rename from 271_phyluce/Cgl-0.60.8-foss-2023a.eb rename to 271_phyluce/unused_econfigs/Cgl-0.60.8-foss-2023a.eb diff --git a/271_phyluce/Clp-1.17.9-foss-2023a.eb b/271_phyluce/unused_econfigs/Clp-1.17.9-foss-2023a.eb similarity index 100% rename from 271_phyluce/Clp-1.17.9-foss-2023a.eb rename to 271_phyluce/unused_econfigs/Clp-1.17.9-foss-2023a.eb diff --git a/271_phyluce/CoinUtils-2.11.10-GCC-12.3.0.eb b/271_phyluce/unused_econfigs/CoinUtils-2.11.10-GCC-12.3.0.eb similarity index 100% rename from 271_phyluce/CoinUtils-2.11.10-GCC-12.3.0.eb rename to 271_phyluce/unused_econfigs/CoinUtils-2.11.10-GCC-12.3.0.eb diff --git a/271_phyluce/Osi-0.108.9-GCC-12.3.0.eb b/271_phyluce/unused_econfigs/Osi-0.108.9-GCC-12.3.0.eb similarity index 100% rename from 271_phyluce/Osi-0.108.9-GCC-12.3.0.eb rename to 271_phyluce/unused_econfigs/Osi-0.108.9-GCC-12.3.0.eb diff --git a/271_phyluce/PuLP-2.8.0-foss-2023a.eb b/271_phyluce/unused_econfigs/PuLP-2.8.0-foss-2023a.eb similarity index 100% rename from 271_phyluce/PuLP-2.8.0-foss-2023a.eb rename to 271_phyluce/unused_econfigs/PuLP-2.8.0-foss-2023a.eb diff --git a/71_GRASP_suite/GRASPsuite-other-jar.eb b/71_GRASP_suite/GRASPsuite-other-jar.eb new file mode 100644 index 00000000..7b4e1b77 --- /dev/null +++ b/71_GRASP_suite/GRASPsuite-other-jar.eb @@ -0,0 +1,39 @@ +easyblock = 'JAR' + +name = 'GRASP-suite' +version = '2022-10-14' +local_commit = '04744b0' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://github.com/bodenlab/GRASP-suite/' + +description = """GRASP-suite is a collection of tools and tutorials to perform and +analyse ancestral sequence reconstruction.""" + +toolchain = SYSTEM +# https://github.com/bodenlab/GRASP/blob/04744b0ea3d802645b73ab7e799145d306ee437c/src/main/resources/grasp-repo/com/asr/bnkit/1.0/bnkit-1.0.jar +source_urls = ['https://github.com/bodenlab/GRASP/blob/%s/src/main/resources/grasp-repo/com/asr/bnkit/1.0/' % local_commit] +sources = [{ + "download_filename": "bnkit-1.0.jar", + "filename": "%(name)s-%(version)s.jar", +}] +checksums = ['3f6009d23c28c5ebfddbc4de5deac8afab42acb512676ae821e57f97850db243'] + +# source_urls = ['https://github.com/bodenlab/GRASP/raw/%s/src/main/resources/lib/' % local_commit] +dependencies = [('Java', '17')] + +postinstallcmds = [ + "mkdir -p %(installdir)s/bin", + "echo '#!/bin/sh' > %(installdir)s/bin/grasp", + "echo 'java -jar -Xmx16g %(installdir)s/%(name)s-%(version)s.jar $@' >> %(installdir)s/bin/grasp", + "chmod a+rx %(installdir)s/bin/grasp" +] + +sanity_check_commands = ["grasp -h"] + +sanity_check_paths = { + 'files': ['bin/grasp', '%(name)s-%(version)s.jar'], + 'dirs': [], +} + +moduleclass = 'bio'