From 668449e3ba8090055de71f8477107bf6327e7507 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 19 Dec 2017 22:03:24 +0100 Subject: [PATCH 1/2] adding easyconfigs: R-bundle-Bioconductor-3.6-intel-2017b-R-3.4.3.eb, MariaDB-connector-c-2.3.4-intel-2017b.eb --- .../MariaDB-connector-c-2.3.4-intel-2017b.eb | 29 ++ ...le-Bioconductor-3.6-intel-2017b-R-3.4.3.eb | 443 ++++++++++++++++++ 2 files changed, 472 insertions(+) create mode 100644 easybuild/easyconfigs/m/MariaDB-connector-c/MariaDB-connector-c-2.3.4-intel-2017b.eb create mode 100644 easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.6-intel-2017b-R-3.4.3.eb diff --git a/easybuild/easyconfigs/m/MariaDB-connector-c/MariaDB-connector-c-2.3.4-intel-2017b.eb b/easybuild/easyconfigs/m/MariaDB-connector-c/MariaDB-connector-c-2.3.4-intel-2017b.eb new file mode 100644 index 000000000000..53ee991660d2 --- /dev/null +++ b/easybuild/easyconfigs/m/MariaDB-connector-c/MariaDB-connector-c-2.3.4-intel-2017b.eb @@ -0,0 +1,29 @@ +easyblock = 'CMakeMake' + +name = 'MariaDB-connector-c' +version = '2.3.4' + +homepage = 'https://downloads.mariadb.org/connector-c/' +description = "MariaDB Connector/C is used to connect applications developed in C/C++ to MariaDB and MySQL databases." + +toolchain = {'name': 'intel', 'version': '2017b'} + +source_urls = ['https://downloads.mariadb.org/f/connector-c-%(version)s'] +sources = ['mariadb-connector-c-%(version)s-src.tar.gz'] +checksums = ['8beb0513da8a24ed2cb47836564c8b57045c3b36f933362f74b3676567c13abc'] + +builddependencies = [('CMake', '3.10.1')] +dependencies = [] + +sanity_check_paths = { + 'files': ['lib/mariadb/libmariadbclient.a', 'lib/mariadb/libmariadb.%s' % SHLIB_EXT], + 'dirs': ['include/mariadb'], +} + +modextrapaths = { + 'CPATH': ['include/mariadb'], + 'LD_LIBRARY_PATH': ['lib/mariadb'], + 'LIBRARY_PATH': ['lib/mariadb'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.6-intel-2017b-R-3.4.3.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.6-intel-2017b-R-3.4.3.eb new file mode 100644 index 000000000000..90e8f1d4ecac --- /dev/null +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.6-intel-2017b-R-3.4.3.eb @@ -0,0 +1,443 @@ +easyblock = 'Bundle' + +name = 'R-bundle-Bioconductor' +version = '3.6' +versionsuffix = '-R-%(rver)s' + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'intel', 'version': '2017b'} + +dependencies = [ + ('R', '3.4.3', '-X11-20171023'), + ('HDF5', '1.10.1'), # for rhdf5 + ('MariaDB-connector-c', '2.3.4'), # for RMySQL +] + +exts_default_options = { + 'source_urls': [ + 'https://bioconductor.org/packages/3.6/bioc/src/contrib/', + 'https://bioconductor.org/packages/3.6/data/annotation/src/contrib/', + 'https://bioconductor.org/packages/3.6/data/experiment/src/contrib/', + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz' +} + +exts_defaultclass = 'RPackage' +exts_filter = ("R -q --no-save", "library(%(ext_name)s)") + +# CRAN packages on which these Bioconductor packages depend are available in R module on which this depends +# !! order of packages is important !! +# packages updated on Dec 19th 2017 +exts_list = [ + ('BiocGenerics', '0.24.0', { + 'checksums': ['517d31c47d7d807170031e116af3ffeba57baca3980ef4d85b37c2ec3bdc9d0f'], + }), + ('Biobase', '2.38.0', { + 'checksums': ['6fa2f0dc214d42f2d0afcc42d2f4da2223ebe67a2f79ff69fba6dc19940cf5b1'], + }), + ('S4Vectors', '0.16.0', { + 'checksums': ['8043a0a9f76e00ab96d4214a0ac888d7cf26c0917bb5b3e48ed5503bc6df480f'], + }), + ('IRanges', '2.12.0', { + 'checksums': ['a51e7219a9adedcc3ec708db570dbe8ed1156b0bd2bc882fbf5577cad3fa0cef'], + }), + ('GenomeInfoDbData', '1.0.0', { + 'checksums': ['d7bb73db4a76960e65c5f6d8ccdcb9480a48cea529a30ea2399f8e4c9887e876'], + }), + ('GenomeInfoDb', '1.14.0', { + 'checksums': ['d7db65fe2a494c3a1a0a087a2776eb69cca914024476b920db8f30356b0415ca'], + }), + ('AnnotationDbi', '1.40.0', { + 'checksums': ['8c5a98056d4ab3c215d6a01b64953589d127be71940cfd0031f694a382c604b6'], + }), + ('zlibbioc', '1.24.0', { + 'checksums': ['22f9bb05a415ae3ce828a904abc0f290aede5ae5fdb212fc75f4c152e08229ff'], + }), + ('XVector', '0.18.0', { + 'checksums': ['b36e985344cc3d033d567e2206029e272e1fc23dc5e0ce66c8149ddcdb1c91c4'], + }), + ('Biostrings', '2.46.0', { + 'checksums': ['f353f6c1fdbc520a685b880ef05f61245f04397adfcaae4c1395e14e1b06e56d'], + }), + ('GenomicRanges', '1.30.0', { + 'checksums': ['4ac4ca12b73bdacc73238c4a9ae37a57c6749f67e0c754697c069e60a5162a83'], + }), + ('BiocParallel', '1.12.0', { + 'checksums': ['0de25aa5c7a1b1cce8da0d5f42a00eaccc50de1edf4ab30174833ecd851dcf8e'], + }), + ('Rsamtools', '1.30.0', { + 'checksums': ['ba2a6f2c13e7d001fb8e1a00bd73130a6a748c8d9daf41a16fceae2d5df1565e'], + }), + ('lambda.r', '1.2', { + 'checksums': ['7dc4188ce1d4a6b026a1b128719ff60234ae1e3ffa583941bbcd8473ad18146f'], + }), + ('futile.options', '1.0.0', { + 'checksums': ['ee84ece359397fbb63f145d11af678f5c8618570971e78cc64ac60dc0d14e8c2'], + }), + ('futile.logger', '1.4.3', { + 'checksums': ['5e8b32d65f77a86d17d90fd8690fc085aa0612df8018e4d6d6c1a60fa65776e4'], + }), + ('DelayedArray', '0.4.1', { + 'checksums': ['8b7ca552d391c58c5899480bbab5bdb975c8ef5f6b2222cc6304fcede313f068'], + }), + ('SummarizedExperiment', '1.8.0', { + 'checksums': ['aeeec5e6a5caacb209ba11e245dc5f454d7359eb04d615860482a00928ca2180'], + }), + ('GenomicAlignments', '1.14.1', { + 'checksums': ['697c17e3a8d4f5480280df6c0b2803c34dcb705a9604ebbde0c76a43b833770c'], + }), + ('ShortRead', '1.36.0', { + 'checksums': ['9f7dbec9d74f16a67403a0f801024fceb637c5ddef2ad97e5716925635b5b31a'], + }), + ('graph', '1.56.0', { + 'checksums': ['c12a519e9984ca2e134a8bef75aac63be59a33691e2206d025e10b88ae944a95'], + }), + ('affyio', '1.48.0', { + 'checksums': ['69aa9239db6ab4a0464138c3fdb21996e93bf38d6ec7fdc870beae36dab8ffdf'], + }), + ('BiocInstaller', '1.28.0', { + 'checksums': ['2d853625dd369d1c7acb6340f1eee6b64245cdf1e4d0786bd9099bbd8e50cfa5'], + }), + ('preprocessCore', '1.40.0', { + 'checksums': ['f022f2b97b8202403d5a28d17b12aec0f46ea1beae7bac5fca8eb5b4e67a2d57'], + }), + ('affy', '1.56.0', { + 'checksums': ['327b0d7ae506632b5c9c0a4f5b527b04fd4bc91be0f63167d3ce15556b9cab4a'], + }), + ('GO.db', '3.5.0', { + 'checksums': ['656055d3e43f9b31c44ea895e831e0917092d5c899fad0e1c6070faa82ada109'], + }), + ('limma', '3.34.4', { + 'checksums': ['6e4c0d5520d7899ac0c0118821efb4173e5d784677a535cbebcf76f464729ded'], + }), + ('RBGL', '1.54.0', { + 'checksums': 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['fc2b2128e2b096c2cb1797796f748a1d1f5471bb1bf6b200dae441ddab671109'], + }), + ('KEGGprofile', '1.20.0', { + 'checksums': ['4dc5aff1528778fad7553517705c9bdb3a9c8054544711bc0b39dd8bede5a54d'], + }), + ('GEOquery', '2.46.13', { + 'checksums': ['cde0b19cdaeb40d917254d6b041b08911bf966319863a24ffde02e3dd32d3cc1'], + }), + ('RSpectra', '0.12-0', { + 'checksums': ['c0a9e7467200e08c945ea2f497a1abb1104d92c48516f5affd6f00f9611d4329'], + }), + ('rARPACK', '0.11-0', { + 'checksums': ['c33401e2e31d272d485ce2ed22e7fe43ac641fd7c0a45a9b848d3ad60df1028a'], + }), + ('mixOmics', '6.3.1', { + 'checksums': ['1883f0c60e4f0dfa0beb62a9b0f377624cc310efef1646b9c4ba57927a5f742f'], + }), + ('minfi', '1.24.0', { + 'checksums': ['27b66608e7aceed1b701b5f85fb35d0356b9c964164b1545cf2afef4b7d265de'], + }), + ('FDb.InfiniumMethylation.hg19', '2.2.0', { + 'checksums': ['605aa3643588a2f40a942fa760b92662060a0dfedb26b4e4cd6f1a78b703093f'], + }), + ('methylumi', '2.24.1', { + 'checksums': ['2c81232bb11f2494a57b70d3664a70f21b31799e96a477ba5c301dc6748f1c16'], + }), + ('lumi', '2.30.0', { + 'checksums': ['52a98db2580c6404ad7b0b674c26c3eb7df629784f63a806ae5dd002cf08c0bf'], + }), + ('widgetTools', '1.56.0', { + 'checksums': ['59bf079ca10fa2af25c778fc9546ab09e205b7e8639e2c966ec96bf251d36a76'], + }), + ('tkWidgets', '1.56.0', { + 'checksums': ['ee39ae67415ea2279df7667d4eda45dcd09efc18f824268bcd7bfbea2d683b7c'], + }), + ('Mfuzz', '2.38.0', { + 'checksums': ['316c3dbca6900baf57ab1b32ce8d86338e51361d976560c32662ade6d11b88a1'], + }), + ('venn', '1.5', { + 'checksums': ['51218e1838b1323fb58635c085ba160036cf8eb5f20080090a28d93a89416855'], + }), + ('maSigPro', '1.50.0', { + 'checksums': ['a06d8b226f47c66dcc4cca92dad943d2899d93617969bd345eee6a41aae3d9b4'], + }), + ('SPIA', '2.30.0', { + 'checksums': ['03f7906c3e07165c1f3021652ea2a015a564fde28b6629384aed6d20bfd95b54'], + }), + ('Gviz', '1.22.2', { + 'checksums': ['6a6b51adcd34bcd993a0030793b484bd9e6e02687d58b4b6905197c46a4a769c'], + }), + ('cummeRbund', '2.20.0', { + 'checksums': ['8034f5509d507057d3ba491ae51b93ee9be303ce51a977ecc5561b7d1d106907'], + }), + ('GenomicFiles', '1.14.0', { + 'checksums': ['3669d0da57f3d4eac35a7736c968d6668c5be5d3825938d90c8e795974ae1c64'], + }), + ('derfinderHelper', '1.12.0', { + 'checksums': ['2b4ca09478fa851e1c6a290bcab429a7760ebbbc27764503bb47d48d12145219'], + }), + ('derfinder', '1.12.0', { + 'checksums': ['b4c510bca06699d1490ff860ea726c214c6a4c5aa4a8e3e18e2848e45cff1d42'], + }), + ('polyester', '1.14.0', { + 'checksums': ['ba4f3221e9a8589cb1ce94b35ebb33f9261b0990b54862032da165eb989db4df'], + }), + ('Rsubread', '1.28.0', { + 'checksums': ['0ce40b2cf49745b008eb696d43cf376cfc6a26fa72aef47dde416201edb36b57'], + }), + ('pcaMethods', '1.70.0', { + 'checksums': ['68aeb04c7b0fffcf2a9e3fce039d69db2c102d122e3b86e01489800e5e192246'], + }), + ('marray', '1.56.0', { + 'checksums': ['2caad6eab11df6f58022ebbfb357e03af6b4cd07945cd415b1f2306f501c8991'], + }), + ('CGHbase', '1.38.0', { + 'checksums': ['9562f906d128261bd2b2239799fa0c0b6654a2452c770b6232f7ad2635dbd63b'], + }), + ('sigaR', '1.26.0', { + 'checksums': ['b380854cbbf25afb685d2ce56e768dae6f12e58451a4425bdd29e2ecd290d2a4'], + }), + ('HCsnip', '1.17.0', { + 'checksums': ['426026207e86888ae16d609b4b1b2170b5ebfe3d6fbb14a151c0ed6f43dd3a81'], + }), + ('metagenomeSeq', '1.20.1', { + 'checksums': ['b713d70b7b2cb8f31e2151ada1cadb7ca46c9c2d2f10fcc3d455831ca9312b96'], + }), + ('gdsfmt', '1.14.0', { + 'checksums': ['498f391047c5dd4907575e488aae4f30b79fdc2c08b432bafff9bc7652313fea'], + }), + ('SNPRelate', '1.12.1', { + 'patches': ['SNPRelate-1.6.5_no-SSE-intr.patch'], + 'checksums': [ + 'd201dd9a09aff86e5d1171d6c7e3c5b7b49d3f7b37c941e8d93cc45a2201c184', # SNPRelate_1.12.1.tar.gz + '258558d4ed00178b2feab0d932955aaeb20a8c08992d88e5ddfc853d4cd79d2a', # SNPRelate-1.6.5_no-SSE-intr.patch + ], + }), + ('rhdf5', '2.22.0', { + 'checksums': ['81110d0f79b2ed1599c90d2a254671ad0eeb07fef92ed66b3456f5f0302aa890'], + }), + ('biomformat', '1.6.0', { + 'checksums': ['7aa98827b119f1cac4b49e777d789ab9f387a791596b05a6844db5a39805476b'], + }), + ('phyloseq', '1.22.3', { + 'checksums': ['c0de813c5eeb68c02d20455552a6feda97a59d2391777dc35a727fcb40115e36'], + }), + ('ALDEx2', '1.10.0', { + 'checksums': ['a3fcadb525906ed3b113a8591c7078c0544f103aa896b2a137dc4052add3c360'], + }), + ('RcppParallel', '4.3.20', { + 'checksums': ['0fac9b63c4c294619388138a048b507efee2e990c447924c309a0421611183c1'], + }), + ('dada2', '1.6.0', { + 'checksums': ['79b65f611f7a4da5b08c9d258ab69540139d8159b24481bbbc2e786604e48e51'], + }), + ('LEA', '2.0.0', { + 'checksums': ['b6e9575b503464a70bb5a04ae828894540795c588194e318599b5655c5173dc0'], + }), + ('tximport', '1.6.0', { + 'checksums': ['505c8d721b09897519cfa0e82fabbfe97a536ce0587c86e59be175185265d8bf'], + }), + ('SingleCellExperiment', '1.0.0', { + 'checksums': ['3a2be57963077d8fac43f40b7213489aae23e713259947db2e8a187e523447e4'], + }), + ('Rhdf5lib', '1.0.0', { + 'checksums': ['3ce431b69998878c074184aece188c3b249ae64ca491be3617162f996f266c4e'], + }), + ('HDF5Array', '1.6.0', { + 'checksums': ['500275365ecf557798e9f40248097a93c7c55520a8e17de9361b2b1d88fa8d4d'], + }), + ('beachmat', '1.0.2', { + 'checksums': ['1ff356bf49dea190aeab405c7785f18e7048eb31b2c7b3b86aa42f5794fccd2c'], + }), + ('scater', '1.6.1', { + 'checksums': ['147ddb0ac3e29c0d1f68ee156a9210bba20f644523acad4d61c3966f677d6072'], + }), + ('scran', '1.6.6', { + 'checksums': ['af36853d8161ae0d95733fe679a67da7a5cfe3bdb66fad862a0f0eef581a48dd'], + }), + ('SC3', '1.7.2', { + 'checksums': ['122124eccbc1b374c8ec6fafa7041598a6513d8d27c4a0ebe6d4f0a222bcdfe4'], + }), + ('ComplexHeatmap', '1.17.1', { + 'checksums': ['9e71eec1020eed2075e87aad460df1c247674b820c0fdae0424d631c4bb9d3f4'], + }), + ('GENIE3', '1.0.0', { + 'checksums': ['a361f25fb8b56114e95fcf9a223956fe6e10213b65094c6bb60281b5299cabd3'], + }), +] + +modextrapaths = {'R_LIBS': ''} + +sanity_check_paths = { + 'files': [], + 'dirs': ['AnnotationDbi', 'BiocInstaller', 'GenomicFeatures'], +} + +moduleclass = 'bio' From 7729134b3819e412fb65173e1974fbb97140b637 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 20 Dec 2017 18:00:04 +0100 Subject: [PATCH 2/2] drop empty list of deps in MariaDB-connector-c easyconfig --- .../MariaDB-connector-c/MariaDB-connector-c-2.3.4-intel-2017b.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MariaDB-connector-c/MariaDB-connector-c-2.3.4-intel-2017b.eb b/easybuild/easyconfigs/m/MariaDB-connector-c/MariaDB-connector-c-2.3.4-intel-2017b.eb index 53ee991660d2..743c1802adeb 100644 --- a/easybuild/easyconfigs/m/MariaDB-connector-c/MariaDB-connector-c-2.3.4-intel-2017b.eb +++ b/easybuild/easyconfigs/m/MariaDB-connector-c/MariaDB-connector-c-2.3.4-intel-2017b.eb @@ -13,7 +13,6 @@ sources = ['mariadb-connector-c-%(version)s-src.tar.gz'] checksums = ['8beb0513da8a24ed2cb47836564c8b57045c3b36f933362f74b3676567c13abc'] builddependencies = [('CMake', '3.10.1')] -dependencies = [] sanity_check_paths = { 'files': ['lib/mariadb/libmariadbclient.a', 'lib/mariadb/libmariadb.%s' % SHLIB_EXT],