From ec3f512691ce0a693be6fe5fc401fa4c9915ceca Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Mon, 9 Dec 2024 15:02:22 +0100 Subject: [PATCH] #467 use v2 + deps + update R-bundle-CRAN --- 467_scNanoGPS/Liqa.eb | 37 + 467_scNanoGPS/R-bundle-CRAN.eb | 3445 +++++++++++++++++++++++++++ 467_scNanoGPS/R-bundle-test-gcmr.eb | 71 + 467_scNanoGPS/annovar.eb | 42 + 467_scNanoGPS/bcftools.eb | 38 + 467_scNanoGPS/lifelines.eb | 43 + 467_scNanoGPS/scNanoGPS.eb | 79 + 467_scNanoGPS/scNanoGPS_v2.eb | 106 + 467_scNanoGPS/tabix.eb | 47 + 9 files changed, 3908 insertions(+) create mode 100644 467_scNanoGPS/Liqa.eb create mode 100644 467_scNanoGPS/R-bundle-CRAN.eb create mode 100644 467_scNanoGPS/R-bundle-test-gcmr.eb create mode 100644 467_scNanoGPS/annovar.eb create mode 100644 467_scNanoGPS/bcftools.eb create mode 100644 467_scNanoGPS/lifelines.eb create mode 100644 467_scNanoGPS/scNanoGPS.eb create mode 100644 467_scNanoGPS/scNanoGPS_v2.eb create mode 100644 467_scNanoGPS/tabix.eb diff --git a/467_scNanoGPS/Liqa.eb b/467_scNanoGPS/Liqa.eb new file mode 100644 index 00000000..416b15b1 --- /dev/null +++ b/467_scNanoGPS/Liqa.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonPackage' + +name = 'Liqa' +version = '1.3.4' + +homepage = "https://pypi.org/project/liqa/" +description = """LIQA (Long-read Isoform Quantification and Analysis) is an Expectation-Maximization +based statistical method to quantify isoform expression and detect differential alternative splicing (DAS) +events using long-read RNA-seq data.""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +# Liqa deps: + # OK Python + # OK Pysam + # OK Numpy + # OK Scipy + # OK UPDATED Lifelines - already lifelines in synthcity not used 2023a + # OK R + # ADD_TO_CRAN gcmr + # OK betareg + +# builddependencies = [('poetry', '1.5.1')] +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('Pysam', '0.22.0'), + ('lifelines', '0.28.0'), + ('R', '4.3.2'), + ('R-bundle-CRAN', '2023.12'), +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +moduleclass = 'bio' diff --git a/467_scNanoGPS/R-bundle-CRAN.eb b/467_scNanoGPS/R-bundle-CRAN.eb new file mode 100644 index 00000000..9a31ca17 --- /dev/null +++ b/467_scNanoGPS/R-bundle-CRAN.eb @@ -0,0 +1,3445 @@ +easyblock = 'Bundle' + +name = 'R-bundle-CRAN' +version = '2023.12' + +homepage = 'https://www.r-project.org/' +description = "Bundle of R packages from CRAN" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('pkgconf', '1.9.5'), + ('Xvfb', '21.1.8'), + ('Autotools', '20220317'), + ('CMake', '3.26.3'), +] + +dependencies = [ + ('R', '4.3.2'), + ('libxml2', '2.11.4'), # for XML + ('GMP', '6.2.1'), # for igraph + ('NLopt', '2.7.1'), # for nlopt + ('FFTW', '3.3.10'), # for fftw + ('libsndfile', '1.2.2'), # for seewave + ('ICU', '73.2'), # for rJava & gdsfmt + ('HDF5', '1.14.0'), # for hdf5r + ('UDUNITS', '2.2.28'), # for units + ('GSL', '2.7'), # for RcppGSL + ('ImageMagick', '7.1.1-15'), + ('GLPK', '5.0'), # for Rglpk + ('nodejs', '18.17.1'), # for V8 (required by rstan) + ('GDAL', '3.7.1'), # for sf + ('MPFR', '4.2.0'), # for Rmpfr + ('PostgreSQL', '16.1'), # for RPostgreSQL +] + +# Some R extensions (mclust, quantreg, waveslim for example) require the math library (-lm) to avoid undefined symbols. +# Adding it to FLIBS makes sure it is present when needed. +preconfigopts = 'export FLIBS="$FLIBS -lm" && ' + +configopts = "--with-pic --enable-threads --enable-R-shlib" +# some recommended packages may fail in a parallel build (e.g. Matrix), and +# we're installing them anyway below +configopts += " --with-recommended-packages=no" + +exts_defaultclass = 'RPackage' + +exts_default_options = { + 'source_urls': [ + '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', +} + +# check whether correct version is installed in extension filter +# (some versions in this bundle may be newer than the ones provided by R) +local_ext_version_check = "pkgver = packageVersion('%(ext_name)s'); if (pkgver != '%(ext_version)s') " +local_stop_msg = "stop('%(ext_name)s %(ext_version)s not installed, found ', pkgver, ' instead')" +exts_filter = ("R -q --no-save", "%s { %s }" % (local_ext_version_check, local_stop_msg)) + +# the dbarts extension needs an additional compiler flag on Arm systems to prevent "incompatible types" errors +# cfr. https://github.com/vdorie/dbarts/issues/66 +if ARCH == 'aarch64': + local_dbarts_preinstallopts = 'sed -i "s|-c partition_neon.c|-flax-vector-conversions -c partition_neon.c|"' + local_dbarts_preinstallopts += ' src/misc/Makefile && ' +else: + local_dbarts_preinstallopts = '' + +# !! order of packages is important !! +# packages updated on 10th December 2023 +exts_list = [ + ('abind', '1.4-5', { + 'checksums': ['3a3ace5afbcb86e56889efcebf3bf5c3bb042a282ba7cc4412d450bb246a3f2c'], + }), + ('magic', '1.6-1', { + 'checksums': ['ca79ec7ae92b736cb128556c081abf547f49956c326e053a76579889cbcb7976'], + }), + ('RcppProgress', '0.4.2', { + 'checksums': ['b1624b21b7aeb1dafb30f092b2a4bef4c3504efd2d6b00b2cdf55dc9df194b48'], + }), + ('lpSolve', '5.6.19', { + 'checksums': ['49d5b49e64c6eba2bc4cea80eb615df21a2d0188b1bbffa05052dc978c94581b'], + }), + ('linprog', '0.9-4', { + 'checksums': ['81a6aa2fdc075f12dc912794d0554f87705a8b872b99c89a90a69ee9ada864b4'], + }), + ('geometry', '0.4.7', { + 'checksums': ['96204205f51b4d63c2e7a7b00365def27d131f3c9ec66db56b510046e5d2013b'], + }), + ('bit', '4.0.5', { + 'checksums': ['f0f2536a8874b6a30b80baefbc68cb21f0ffbf51f3877bda8038c3f9f354bfbc'], + }), + ('filehash', '2.4-5', { + 'checksums': ['3b1ee2794dd61e525ee44db16611c65957691d77bb26ae481eba988bb55da22c'], + }), + ('ff', '4.0.9', { + 'checksums': 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['45d374ebfdcc2c9f6cc738d196caf83a2297ed2aefe2cc99007fcbeb78a61c34'], + }), + ('clustree', '0.5.1', { + 'checksums': ['b5f2496e596e3fd140ace69c4837085e13f3abb850f5eb57d496380691fdd117'], + }), + ('tweedie', '2.3.5', { + 'checksums': ['983c745fee5a780d46e8dd04c2eb1c10cb2e222d3679654f0d6934d3db7b1c3e'], + }), + ('RcppGSL', '0.3.13', { + 'checksums': ['fe5e73bc119c6424e1a40b6fea17417a7bba93e81dbe9b7cf86dde9b8e8d93e7'], + }), + ('mvabund', '4.2.1', { + 'checksums': ['ed6946c95609443584081100cd38624d2309f7f5d210fd4b8ec12ad25bd27a06'], + }), + ('fishMod', '0.29', { + 'checksums': ['5989e49ca6d6b2c5d514655e61f75b019528a8c975f0d6056143f17dc4277a5d'], + }), + ('alabama', '2023.1.0', { + 'checksums': ['925f67c72d9cdb677105377777bd09e9b56a61573bea7e3f69e0a49595c7bf1c'], + }), + ('gllvm', '1.4.3', { + 'checksums': ['63b77040e9cf2694882d1d80a3bc3030b3a348819ea38e6728417e4c5de07ecc'], + }), + ('grpreg', '3.4.0', { + 'checksums': ['fd57d20baf63d2cc5821998bca5c3fdcbe46c933c9553caa492911b12654d6ad'], + }), + ('trust', '0.1-8', { + 'checksums': ['952e348b62aec35988b103fd152329662cb6a451538f184549252fbf49d7dcac'], + }), + ('lpSolveAPI', '5.5.2.0-17.11', { + 'checksums': ['b08d6cae4fc17575adf5df0113ea5f4f819bb2c7f87987e0d66c8eabfc933fa4'], + }), + ('ergm', '4.5.0', { + 'checksums': ['3372c7bd35b640518d65a62615cb7029652a65fe2851748847f1c16b657b6351'], + }), + ('networkLite', '1.0.5', { + 'checksums': ['aaab55d4f8f0b330fe7c1ecbab3c44746c52c2fda99c53c6b46042bb8775718b'], + }), + ('networkDynamic', '0.11.3', { + 'checksums': ['2c664fd0d85c0cdc099480d67a18e6afbb0cc1036963b6664a8a756874648e5b'], + }), + ('ergm.multi', '0.2.0', { + 'checksums': ['13e27ba59b087f09cfb3dc6fccaa360e4ae0159f13e7a20d2c3306b5fe74fb5a'], + }), + ('tergm', '4.2.0', { + 'checksums': ['dcf5a26cc2c4d165766706af08f8ea4f36e328158f5b682490c2a351f7fbda69'], + }), + ('ergm.count', '4.1.1', { + 'checksums': ['446893614ad8b41aa39c37c2bf45a167f575536bb6778b8ad1fbcddb7b934932'], + }), + ('tsna', '0.3.5', { + 'checksums': ['4ee2f773d573f0f4bd93131156fdccf01d7f1a3f725eff3e885021098c6bff65'], + }), + ('statnet', '2019.6', { + 'checksums': ['0903e1a81ed1b6289359cefd12da1424c92456d19e062c3f74197b69e536b29d'], + }), + ('aggregation', '1.0.1', { + 'checksums': ['86f88a02479ddc8506bafb154117ebc3b1a4a44fa308e0193c8c315109302f49'], + }), + ('ComICS', '1.0.4', { + 'checksums': ['0af7901215876f95f309d7da6e633c38e4d7faf04112dd6fd343bc15fc593a2f'], + }), + ('dtangle', '2.0.9', { + 'checksums': ['c375068c1877c2e8cdc5601cfd5a9c821645c3dff90ddef64817f788f372e179'], + }), + ('mcmc', '0.9-8', { + 'checksums': ['6a06440d4b58e8a7f122747d92046ff40da4bb58a20bf642228a648a0c826ea7'], + }), + ('MCMCpack', '1.6-3', { + 'checksums': ['cb14ba20690b31fd813b05565484c866425f072a5ad99a5cbf1da63588958db3'], + }), + ('shinythemes', '1.2.0', { + 'checksums': ['37d68569ce838c7da9f0ea7e2b162ecf38fba2ae448a4888b6dd29c4bb5b2963'], + }), + ('csSAM', '1.2.4', { + 'checksums': ['3d6442ad8c41fa84633cbbc275cd67e88490a160927a5c55d29da55a36e148d7'], + }), + ('bridgedist', '0.1.2', { + 'checksums': ['7210c97fc864e78ea8502067359d642bbd95bf2df30d33da193fc5c004e45baf'], + }), + ('asnipe', '1.1.17', { + 'checksums': ['e7b4010fa1adf27534420db2971dae3c63190920a4323c86fd586842e22d9b07'], + }), + ('liquidSVM', '1.2.4', { + # Don't add optimization flags by liquidSVM which may not be known e.g. on PPC + 'patches': ['liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch'], + 'preinstallopts': 'LIQUIDSVM_TARGET="empty"', + 'checksums': [ + {'liquidSVM_1.2.4.tar.gz': '15a9c7f2930e2ed3f4c5bcd9b042884ea580d2b2e52e1c68041600c196046aba'}, + {'liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch': + '46b09e441c3b59af535f20d8db0dee7f1d6a7ddd511175d252115b53cb8b86f8'}, + ], + }), + ('oddsratio', '2.0.1', { + 'checksums': ['2097e7a8bf623379d55652de5dce4946d05163e85d30df50dc19055962bf60b5'], + }), + ('mltools', '0.3.5', { + 'checksums': ['7093ffceccdf5d4c3f045d8c8143deaa8ab79935cc6d5463973ffc7d3812bb10'], + }), + ('h2o', '3.42.0.2', { + 'checksums': ['9aae531f4eb3ed90b5d3e31a9030ba0ca7c6bdc6e3c84aec2a5c4e3eb562929b'], + }), + ('mlegp', '3.1.9', { + 'checksums': ['63296d17a162fdce0958b10f45cb7d5dab4b3ee29340528d33cedcae08a040b3'], + }), + ('itertools', '0.1-3', { + 'checksums': ['b69b0781318e175532ad2d4f2840553bade9637e04de215b581704b5635c45d3'], + }), + ('missForest', '1.5', { + 'checksums': ['417055a03b02ad8359cf1bdc8f89d49531a3a8ee2c98edf90c8a01432f44838d'], + }), + ('bartMachineJARs', '1.2.1', { + 'checksums': ['9f7a20acf4aec249e16f83d81f5ec796aa718deb1b8bc24393fc0421eb8ce1c0'], + }), + ('bartMachine', '1.3.4.1', { + 'checksums': ['3b0a5250f5425a8efe460adcb58ea1342f1d845ae3a8db29dbf4806653884b89'], + }), + ('lqa', '1.0-3', { + 'checksums': ['3889675dc4c8cbafeefe118f4f20c3bd3789d4875bb725933571f9991a133990'], + }), + ('PresenceAbsence', '1.1.11', { + 'checksums': ['c63a6453783865b7c69c580a09a769e99390dd8b2e0f63e48fbfc86da3bee4b7'], + }), + ('GUTS', '1.2.5', { + 'checksums': ['9d983a566daa07d3e0036fe7011efe94f29e31a611493ba16bd316b61730a7b7'], + }), + ('GenSA', '1.1.10.1', { + 'checksums': ['9093384941b5626aae2acf4835b591875193a6000d1f0b212abeaf682652949b'], + }), + ('parsedate', '1.3.1', { + 'checksums': ['1fc31ab9813b61680abf4f4c2705b8f484d56d1d3ef256df84b342b628b6d1b1'], + }), + ('circular', '0.5-0', { + 'checksums': ['4bf4da5de29e555d1a7ae7ea64f8a5dda037e5c423f1078944f0bbb6eb9a7b92'], + }), + ('cobs', '1.3-5', { + 'checksums': ['7fae7da8f940975d544120c836e2d3b874f9b0cbab9631851ce986709f51c611'], + }), + ('resample', '0.6', { + 'checksums': ['1b958009b18c92a47971847c782af76952ea4e85d5f1e3e1e70fa35c67b95265'], + }), + ('MIIVsem', '0.5.8', { + 'checksums': ['a908f51e1598290d25864c358d57201bd50c1c40775d4d0405cbc8077bee61e1'], + }), + ('medflex', '0.6-10', { + 'checksums': ['bd89a8fe939f3becd71a9dab30fe27fa43c96572d8309d2c1a70633117d4cb33'], + }), + ('Rserve', '1.8-13', { + 'checksums': ['7e5d312fca8029d746f60e7d9e701129561942f97dfc33b036b123f159d69a4c'], + }), + ('spls', '2.2-3', { + 'checksums': ['bbd693da80487eef2939c37aba199f6d811ec289828c763d9416a05fa202ab2e'], + }), + ('Boruta', '8.0.0', { + 'checksums': ['38e75b1ebc8b2d1c54b3373a42529b819c7b4773fd4932f57bc9701d1e3e3dc7'], + }), + ('dr', '3.0.10', { + 'checksums': ['ce523c1bdb62a9dda30afc12b1dd96975cc34695c61913012236f3b80e24bf36'], + }), + ('CovSel', '1.2.1', { + 'checksums': ['b375d00cc567e125ff106b4357654f43bba3abcadeed2238b6dea4b7a68fda09'], + }), + ('tmle', '2.0.0', { + 'checksums': ['8693cab745d426260227d522d9113078d720b1ac0eb0931a47fa8f74aab82fa7'], + }), + ('ctmle', '0.1.2', { + 'checksums': ['e3fa0722cd87aa0e0b209c2dddf3fc44c6d09993f1e66a6c43285fe950948161'], + }), + ('BayesPen', '1.0', { + 'checksums': ['772df9ae12cd8a3da1d5b7d1f1629602c7693f0eb03945784df2809e2bb061b0'], + }), + ('inline', '0.3.19', { + 'checksums': ['0ee9309bb7dab0b97761ddd18381aa12bd7d54678ccd7bec00784e831f4c99d5'], + }), + ('BMA', '3.18.17', { + 'checksums': ['6d8c514fa179f8a48c2105b551a8a08e28ea4375d06150a4b8ab4ccda577daf5'], + }), + ('BCEE', '1.3.2', { + 'checksums': ['f0e0a6a4eb11213073aa2f0cd6c76d87e8b3965124d8ca509538eb3c128533a0'], + }), + ('bacr', '1.0.1', { + 'checksums': ['c847272e2c03fd08ed79b3b739f57fe881af77404b6fd087caa0c398c90ef993'], + }), + ('clue', '0.3-65', { + 'checksums': ['bdf8fdd35fb2b1c65d09766da79d930fa664a00aa497f03b636400eecb623ef8'], + }), + ('bdsmatrix', '1.3-6', { + 'checksums': ['f9c871d54378408902931792b3dbf8bda863d6aa67af6a0472a6ec1c420760bc'], + }), + ('fftwtools', '0.9-11', { + 'checksums': ['f1f0c9a9086c7b2f72c5fb0334717cc917213a004eaef8448eab4940c9852c7f'], + }), + ('imagerExtra', '1.3.2', { + 'checksums': ['0ebfa1eabb89459d774630ab73c7a97a93b9481ea5afc55482975475acebd5b8'], + }), + ('MALDIquant', '1.22.1', { + 'checksums': ['0a52a55dbe76a7e7ca50c5555fea4381eeda0c215c66e420d8dc9bfd2992411c'], + }), + ('threejs', '0.3.3', { + 'checksums': ['76c759c8b20fb34f4f7a01cbd1b961296e1f19f4df6dded69aae7f1bca80219c'], + }), + ('LaplacesDemon', '16.1.6', { + 'checksums': ['57b53882fd7a195b38bbdbbf0b17745405eb3159b1b42f7f11ce80c78ab94eb7'], + }), + ('rda', '1.2-1', { + 'checksums': ['37038a9131c9133519f5e64fa1a86dbe28b21f519cf6528503234648a139ae9a'], + }), + ('sampling', '2.10', { + 'checksums': ['fdec976ec0abfb5c690049d76f89ebcb8ab3650e2eb28a5b54c3984d17372775'], + }), + ('lda', '1.4.2', { + 'checksums': ['5606a1e1bc24706988853528023f7a004c725791ae1a7309f1aea2fc6681240f'], + }), + ('jiebaRD', '0.1', { + 'checksums': ['045ee670f5378fe325a45b40fd55136b355cbb225e088cb229f512c51abb4df1'], + }), + ('jiebaR', '0.11', { + 'checksums': ['adde8b0b21c01ec344735d49cd33929511086719c99f8e10dce4ca9479276623'], + }), + ('hdm', '0.3.1', { + 'checksums': ['ba087565e9e0a8ea30a6095919141895fd76b7f3c05a03e60e9e24e602732bce'], + }), + ('abe', '3.0.1', { + 'checksums': ['66d2e9ac78ba64b7d27b22b647fc00378ea832f868e51c18df50d6fffb8029b8'], + }), + ('SignifReg', '4.3', { + 'checksums': ['f755808fcb618582acb862729b20e267d9c2214f22e6e7a0c8d29073d8faa7b8'], + }), + ('bbmle', '1.0.25.1', { + 'checksums': ['d92a0cf819fe4c08b8eb17f5e03275c8accde7f3b54f990cbba5ab926575b60b'], + }), + ('emdbook', '1.3.13', { + 'checksums': ['26044b7ea1b42304b4dfde48afa94dd487acf979da4db2bf670ba41222083c19'], + }), + ('SOAR', '0.99-11', { + 'checksums': ['d5a0fba3664087308ce5295a1d57d10bad149eb9771b4fe67478deae4b7f68d8'], + }), + ('rasterVis', '0.51.6', { + 'checksums': ['61bd0d19d045b50c6764f3a7c95ce1e734af9e5f964449825d002afe02109489'], + }), + ('tictoc', '1.2', { + 'checksums': ['f05ea4b4142a90b0dc5d10356be3748625ef86bbd0e4399c56455654165ff20c'], + }), + ('ISOcodes', '2023.12.07', { + 'checksums': ['73631fec5822d256e91d7b929ab7f5d7c2312749990d4031f65e0408c366d90e'], + }), + ('stopwords', '2.3', { + 'checksums': ['c5ec1c6ab1bad1786d87d7823d4b63abc94d2fd84ed7d8e985906e96fb6321b2'], + }), + ('janeaustenr', '1.0.0', { + 'checksums': ['b4c32ee1395ee4a8efe714c535c0fe578b0dbf5f3bb85b41fa5cc87569b8e8aa'], + }), + ('SnowballC', '0.7.1', { + 'checksums': ['753cf13f3206751662c03b1cf39bce9e680024f6d9f8503b836a83797181c034'], + }), + ('tokenizers', '0.3.0', { + 'checksums': ['24571e4642a1a2d9f4f4c7a363b514eece74788d59c09012a5190ee718a91c29'], + }), + ('hunspell', '3.0.3', { + 'checksums': ['fdaa1473a62dff2a5923b9bd958d87e546069ca22ce113f44e88c761338442f3'], + }), + ('topicmodels', '0.2-15', { + 'checksums': ['71b50f78e4d7b95b5c3663d766eb15ad2061cc49d58436dc3aa56960cdaf77d0'], + }), + ('tidytext', '0.4.1', { + 'checksums': ['526750a2cc8ac7b65be1093f4c9186aa27f0a22f00023a6d6b3b878e1310c815'], + }), + ('splitstackshape', '1.4.8', { + 'checksums': ['656032c3f1e3dd5b8a3ee19ffcae617e07104c0e342fc3da4d863637a770fe56'], + }), + ('grImport2', '0.3-1', { + 'checksums': ['216a1a5bb18c7a7dfb13c6c162228c6c81c45408f04d7784b6e60ae6cd4745d2'], + }), + ('preseqR', '4.0.0', { + 'checksums': ['0143db473fb9a811f9cf582a348226a5763e62d9857ce3ef4ec41412abb559bc'], + }), + ('idr', '1.3', { + 'checksums': ['6b3910dc48495439cd01828f8999823864a6712f73560ee3e6c903065c67d1e4'], + }), + ('entropy', '1.3.1', { + 'checksums': ['6f5a89f5ce0e90cbed1695b81259326c976e7a8f538157e223ee5f63b54412b8'], + }), + ('kedd', '1.0.3', { + 'checksums': ['38760abd8c8e8f69ad85ca7992803060acc44ce68358de1763bd2415fdf83c9f'], + }), + ('HiddenMarkov', '1.8-13', { + 'checksums': ['7186d23e561818f3e1f01376a4fb2af9ccee775ce5afc1e3175f3b07a81db515'], + }), + ('lmerTest', '3.1-3', { + 'checksums': ['35aa75e9f5f2871398ff56a482b013e6828135ef04916ced7d1d7e35257ea8fd'], + }), + ('loo', '2.6.0', { + 'checksums': ['66da60fdf53a62cbc93797fa696a4cc43bce77f1721dd4bc1a58d25b3f981210'], + }), + ('RcppParallel', '5.1.7', { + 'checksums': ['f9c30eb9ce1abffc590825d513d6d28dcbe970e36032dd7521febf04e905b29c'], + }), + ('StanHeaders', '2.26.28', { + 'checksums': ['938a8d96d3a64357b5fee73eea2923a2a2292a062ff516ea8c720756ec7e3de8'], + }), + ('V8', '4.4.1', { + 'installopts': '--configure-vars="INCLUDE_DIR=$CPATH LIB_DIR=$LIBRARY_PATH"', + 'preinstallopts': "export CPATH=$EBROOTNODEJS/include/node:$CPATH && ", + 'checksums': ['5b6dd6133d83f3cc7297d0369706070f26c376d6ce6fb4cfcf2ad5308abd3a89'], + }), + ('QuickJSR', '1.0.8', { + 'checksums': ['7697faa26d7c67b7d218ae6be74c86e7249842d6f0ea8a3932920825398a9e81'], + }), + ('rstan', '2.32.3', { + 'checksums': ['a29d9e1abf6d7c7b5ce98e10e60f14f18bad076aff4c7affa4b6263945ba549d'], + }), + ('Rborist', '0.3-5', { + 'checksums': ['30cf41ae646e53ef5e4be0c924eca9c783ccec9e771aeba1429f801009be8abc'], + }), + ('VSURF', '1.2.0', { + 'checksums': ['c027b1e19762f1eaf4a559c2592f3530210fefd21ee3d7c787c73b776c683393'], + }), + ('mRMRe', '2.1.2.1', { + 'checksums': ['d53c392e82a437005b71d0e8b97350d0237608fffafe087700fe7f6770167fd9'], + }), + ('dHSIC', '2.1', { + 'checksums': ['94c86473790cf69f11c68ed8ba9d6ae98218c7c69b7a9a093f235d175cf83db0'], + }), + ('ggsci', '3.0.0', { + 'checksums': ['8901316516d78f82a2a8685d93ba479424bcfd8cb5e28a28adbd50e68964e129'], + }), + ('ggsignif', '0.6.4', { + 'checksums': ['112051af425a0c0f2998ce187dacad066bc16f55af01e3e7b76d62ff6954b20a'], + }), + ('corrplot', '0.92', { + 'checksums': ['e8c09f963f9c4837036c439ebfe00fa3a6e462ccbb786d2cf90850ddcd9428bd'], + }), + ('rstatix', '0.7.2', { + 'checksums': ['e0c6f5ab1d9c5d84713defabc5d149aad3d55944cffdb903cc128b694e5221a1'], + }), + ('ggfan', '0.1.3', { + 'checksums': ['5c888b203ecf5e3dc7a317a790ca059c733002fbca4b4bc1a4f62b7ded5f70dc'], + }), + ('ggpubr', '0.6.0', { + 'checksums': ['2e6ec5d8151991d17ef8832259cf545fa0d1a50b326ba8c1c4657700171df774'], + }), + ('yaImpute', '1.0-33', { + 'checksums': ['58595262eb1bc9ffeeadca78664c418ea24b4e894744890c00252c5ebd02512c'], + }), + ('intrinsicDimension', '1.2.0', { + 'checksums': ['6cc9180a83aa0d123f1e420136bb959c0d5877867fa170b79536f5ee22106a32'], + }), + ('leiden', '0.4.3.1', { + 'checksums': ['a9ecbbcfa2724d8fdd0133af569278e036b25b6e2cbb23d453092cc6b3fc30e2'], + }), + ('sctransform', '0.4.1', { + 'checksums': ['5f6be7f8be543e4c32c8007207b603a750881459370b7bb5afd63e8c8fabf171'], + }), + ('packrat', '0.9.2', { + 'checksums': ['69df5943257e6c4d06f3d907241b668b53dedece72158ca935260b8b8e1672d7'], + }), + ('colourpicker', '1.3.0', { + 'checksums': ['c7f2618cd1ae1f7ac15aee072c648e6494dfff6714e13dc7cd1da993d1102510'], + }), + ('ggExtra', '0.10.1', { + 'checksums': ['6879edfe8e3905a2c299cbd18777422223ad30042bc6e20614ca5109a75de82c'], + }), + ('findpython', '1.0.8', { + 'checksums': ['0f8a90cbafd4949c0333a86808383a358fb7ec3268953d8a4887d5d22264cdb7'], + }), + ('argparse', '2.2.2', { + 'checksums': ['b62c9bf5e6ca35fb7a2e614a916815c04cbf6c6db3f89f99b4df76470a4a856d'], + }), + ('intergraph', '2.0-3', { + 'checksums': ['354640a8ac4a1186e6d229b6c25f0535be3e456c13b1e7224a1632d3a346a7e8'], + }), + ('ggnetwork', '0.5.12', { + 'checksums': ['74368662c1a225cdefc8addf606b398f14dafeff03faac56c15aa5e14819e9cd'], + }), + ('qqman', '0.1.9', { + 'checksums': ['3f6a931771d375174b78f220471ddd601def9b5c69631931b0992ebbc8c5bc13'], + }), + ('rstantools', '2.3.1.1', { + 'checksums': ['f260ee54c11461d0f80f447e6fa6909337ede09806cd48f4a89ae9d59804e22e'], + }), + ('distributional', '0.3.2', { + 'checksums': ['c883d633398233aee5a8ca6b587687f765bdfe0732a84e4961e7f71ac0d008f8'], + }), + ('posterior', '1.5.0', { + 'checksums': ['4a10307fcae321f2cd4ca7871504a0c6c9152b8473dc9a033721e8dcda18e2de'], + }), + ('bayesplot', '1.10.0', { + 'checksums': ['bb4cb92b1ae4cf8ae5f4b5cb092aba34af3d820d137e1f2265cca8f3e85113ff'], + }), + ('dygraphs', '1.1.1.6', { + 'checksums': ['c3d331f30012e721a048e04639f60ea738cd7e54e4f930ac9849b95f0f005208'], + }), + ('renv', '1.0.3', { + 'checksums': ['985a1432144a662d34af4b55a3e38c4fc030551ba077f68541af91a1a70f5eb4'], + }), + ('rsconnect', '1.1.1', { + 'checksums': ['77bce6f08ed376be1028b05db3526bb4587aa024d86b9117ab30af177c5608ed'], + }), + ('shinystan', '2.6.0', { + 'checksums': ['a084856a2d66d8744f2c72e3e19ca35e600a508ed7ef1f7ebed8c7fc0738d529'], + }), + ('optimx', '2023-10.21', { + 'checksums': ['0d732d5604c26af59cfb95b80ed4e226c9c10422e2d82a6cc06b92f9ba6a44b5'], + }), + ('gamm4', '0.2-6', { + 'checksums': ['57c5b66582b2adc32f6a3bb6a259f5b95198e283a96d966a6007e8e48b380c89'], + }), + ('memisc', '0.99.31.6', { + 'checksums': ['52336b4ffc6e60c3ed10ccc7417231582b0d2e4c5c3b2184396a7d3ca9c1d96e'], + }), + ('mclogit', '0.9.6', { + 'checksums': ['9adc5f6d8649960abe009c30d9b4c448ff7d174c455a594cbf104a33d5a36f69'], + }), + ('projpred', '2.7.0', { + 'checksums': ['b9e8336c1da7eea958e8aca8ecdb9e2aea1a3d9a3032bb288914db0fd69ecd37'], + }), + ('brms', '2.20.4', { + 'checksums': ['00a6f3ea690c4e6b3e645e0a366d8a93c9bd51151b9376d01011ab95e332072f'], + }), + ('drgee', '1.1.10', { + 'checksums': ['e684f07f7dfec922380d4202922c11094f859721f77b31ff38b0d35d0f42c743'], + }), + ('stdReg', '3.4.1', { + 'checksums': ['285335dbe29b6898641e1151ab2f06acf76c6f4d6fbeadd66d151c25d7e38a74'], + }), + ('mcmcse', '1.5-0', { + 'checksums': ['4a820dc22c48efd32b7f9d1e1b897b4b3f165cd64b2ff85ba7029621cf9e7463'], + }), + ('copCAR', '2.0-4', { + 'checksums': ['8b4ed53c58a665f70e48bdca689a992a81d5ecb5a6051ca7361d3870e13c77f3'], + }), + ('batchmeans', '1.0-4', { + 'checksums': ['8694573009d9070a76007281407d3314da78902e122a9d8aec1f819d3bbe562c'], + }), + ('ngspatial', '1.2-2', { + 'checksums': ['3fa79e45d3a502a58c1454593ec83dfc73144e92b34c14f617a6126557dd0d26'], + }), + ('BIGL', '1.8.0', { + 'checksums': ['52a3eace87d73e3088d2eacc37c1840ca0436f6060498cc2520a2d9f9955dff3'], + }), + ('drugCombo', '1.2.1', { + 'checksums': ['9a605c655c159604033558d757711e6d83d33dfc286c1280f722d4cb7d130f80'], + }), + ('betareg', '3.1-4', { + 'checksums': ['5106986096a68b2b516215968158589b71969ce7912879253d6e930355a18101'], + }), + ('unmarked', '1.3.2', { + 'checksums': ['a1d21619c8627419e09646cc12e09457c0ea8989caf2e674d032e59b310cf883'], + }), + ('maxlike', '0.1-10', { + 'checksums': ['0c0af4c44140e6037b6b9700013fe2b87f750b4af41b7646b37e16bd7feb5133'], + }), + ('coxme', '2.2-18.1', { + 'checksums': ['aef691d74ee75095c43d7b6ab27e01641382cfb349a8eefad972c745ac0531f5'], + }), + ('AICcmodavg', '2.3-3', { + 'checksums': ['4055b5f1fc12917b9f812c056e6a2dbf23bbd0169e468f567306ddf29d699f7a'], + }), + ('pacman', '0.5.1', { + 'checksums': ['9ec9a72a15eda5b8f727adc877a07c4b36f8372fe7ed80a1bc6c2068dab3ef7c'], + }), + ('spaa', '0.2.2', { + 'checksums': ['a5a54454d4a7af473ce797875f849bd893005cb04325bf3e0dbddb19fe8d7198'], + }), + ('maxnet', '0.1.4', { + 'checksums': ['fd21e5ecf3c1ac00ef1bbe79fab4cdd62789e0c4c45f126f1b64bda667238216'], + }), + ('oai', '0.4.0', { + 'checksums': ['f540de066de5538e303cd535cbd2e771b40474bc2c6e8d08a4894a868543ee33'], + }), + ('wellknown', '0.7.4', { + 'checksums': ['483e6fc43edf09ed583e74ce5ca7e2d7838ef8a32291e06d774c37546eed1a34'], + }), + ('rgbif', '3.7.8', { + 'checksums': ['c0d3b84ce6fbbadf007c16ea93c3037faf451736d8ced5b0b9f529b53685b1a3'], + }), + ('rgdal', '1.6-7', { + 'checksums': ['555cedfdadb05db90b061d4b056f96d8b7010c00ea54bc6c1bbcc7684fadae33'], + }), + ('rgeos', '0.6-4', { + 'checksums': ['9d03c4de96fd3fad55ff8d1ff8113dcaaa00f15d9d0588e54c9f91751bcede11'], + }), + ('mapproj', '1.2.11', { + 'checksums': ['db2d201cc939de26717566066bf44225a967ccde6fc34731af845f03c086347d'], + }), + ('rbison', '1.0.0', { + 'checksums': ['9957e5f85ce68f5dd0ddc3c4b2b3c9d2f52d6f37587e1022ab8a44863534a83c'], + }), + ('rebird', '1.3.0', { + 'checksums': ['b238d3f246aa0249145894e1f3a90f46902f6615fc2f23b24c99bb5feecc55d3'], + }), + ('rvertnet', '0.8.2', { + 'checksums': ['2de9a3ec33a213c7592b49cca1d510a25aef0625369376d9b1b4e5d0da519226'], + }), + ('ridigbio', '0.3.7', { + 'checksums': ['af2a90a8a90fbede4cf2178b758f00cc13066f4d0bd87dac8d156809050a6d59'], + }), + ('spocc', '1.2.2', { + 'checksums': ['af4b398dc02522629b9fee697ccf640b7654330419a8f94cb5d1c7d17c8784fc'], + }), + ('spThin', '0.2.0', { + 'checksums': ['2e997afb79a2a990eded34c71afaac83986669cfa9ac51b15ae3f2b558902048'], + }), + ('RPostgreSQL', '0.7-5', { + 'checksums': ['6b5401ee55bd948ae7bc84520d789ceb422533a7d5e5bd6e10e3b54447f29fa1'], + }), + ('fasterize', '1.0.5', { + 'checksums': ['d44f101aec29aee285c4c7b578e26d11b6add423336ace90a7c22e07cfc1c3b4'], + }), + ('BIEN', '1.2.6', { + 'checksums': ['fa7a25d89f26c10686fb4ab4d0aa704beb50dc44b173ff56abe4ab3e5991f99f'], + }), + ('rangeModelMetadata', '0.1.5', { + 'checksums': ['289620500522d489aafbb03c85f68182ef0a6701fed5f9d09b55fae337e2647b'], + }), + ('ENMeval', '2.0.4', { + 'checksums': ['6d9f3c460fa7ab3131cede904fcb9280cf69f4fdd43f67115a3abcb8ed5b64d1'], + }), + ('plotmo', '3.6.2', { + 'checksums': ['cde33a8ec558b12d8e11d7d0531e73f6678a25ee589b79897d2fc425a3fd353c'], + }), + ('earth', '5.3.2', { + 'checksums': ['c844d75edf9a2706a911bb05ed4287aad9acf6f3fed357e037763a300eac0bea'], + }), + ('mda', '0.5-4', { + 'checksums': ['f25f7f28807d0fa478b1b55eb9d026ebc30577d9d5ff288f9abfe1f3fdb8a759'], + }), + ('xgboost', '1.7.6.1', { + 'checksums': ['f23dd6b6ca7a58ef3236d8bdc7b4928591507cf41133fc8053d32ab91b3d3d60'], + }), + ('biomod2', '4.2-4', { + 'checksums': ['c28163075df90a90fc1939e9ff24d40bace7de611ff7ddfe027e0ff980e7c64f'], + }), + ('poLCA', '1.6.0.1', { + 'checksums': ['ed8c60a42bff0402c9ba2f9ce1422dd171e711c1a64498c4d96010ddb29f6b16'], + }), + ('PermAlgo', '1.2', { + 'checksums': ['aa2c774d6c6dcfeec882c1936e8723ef49bd36030fb10c17ca60bb9d4a519443'], + }), + ('coxed', '0.3.3', { + 'checksums': ['d0d6cb8fea9516b3c63b34d0d81f3804c18a07f97a83e51555575c8ed4c75626'], + }), + ('testit', '0.13', { + 'checksums': ['90d47168ab6bdbd1274b600b457626ac07697ce09792c92b2043be5f5b678d80'], + }), + ('NISTunits', '1.0.1', { + 'checksums': ['eaccd68db5c73d6a089ce5b323cdd51bc6a6a58ce467987158ba8c9be6a0a94e'], + }), + ('celestial', '1.4.6', { + 'checksums': ['9f647f41465ac65b254717698f1978871c378ad8e6ccaa693abf579437069abe'], + }), + ('RPMM', '1.25', { + 'checksums': ['f04a524b13918062616beda50c4e759ce2719ce14150a0e677d07132086c88c8'], + }), + ('RefFreeEWAS', '2.2', { + 'checksums': ['de2812f166caabf6ea01c0533402e5cd9d8a525a2a7583e4757decf22319caab'], + }), + ('wordcloud', '2.6', { + 'checksums': ['53716954430acd4f164bfd8eacd7068a908ee3358293ded6cd992d53b7f72649'], + }), + ('JADE', '2.0-4', { + 'checksums': ['d4b3d65a33cae454d3ab13343bceabfb3f6b8004ac64ae7bd86dee92a1cd2055'], + }), + ('awsMethods', '1.1-1', { + 'checksums': ['50934dc20cf4e015f1304a89de6703fed27e7bd54c6b9fc9fb253cdf2ecb7541'], + }), + ('aws', '2.5-3', { + 'checksums': ['154ed68785de8c4a02db1916dfe50862cf544865901936e864207ada777e5108'], + }), + ('ruv', '0.9.7.1', { + 'checksums': ['a0c54e56ba3d8f6ae178ae4d0e417a79295abf5dcb68bbae26c4b874734d98d8'], + }), + ('mhsmm', '0.4.21', { + 'checksums': ['293544afb194934b1d58cf88c6f8c372f537745514b6e428cf83ae62e87d2bba'], + }), + ('dbarts', '0.9-25', { + 'checksums': ['39a78228ead17c92bd88fe5f959c888412a22a7cbbc0edfa9c09072b4182d870'], + 'preinstallopts': local_dbarts_preinstallopts, + }), + ('proftools', '0.99-3', { + 'checksums': ['e034eb1531af54013143da3e15229e1d4c2260f8eb79c93846014db3bdefb724'], + }), + ('NCmisc', '1.2.0', { + 'checksums': ['26fcfbc79810f23a28389a5ce5519e6ddc2470c5e924ba8cf4dd19a1b0fd9f83'], + }), + ('reader', '1.0.6', { + 'checksums': ['905c7c5a1b035ac8213fc533fa26e511abfeea40bd22e3edfde42a49074e88f4'], + }), + ('gnumeric', '0.7-10', { + 'checksums': ['f6fcd9012f2fa777127c86ba520d8dc834f4ea746a6e29623edd072479191c75'], + }), + ('tcltk2', '1.2-11', { + 'checksums': ['ad183ae3b7190501504a0589e0b3be480f04267303e3384fef00987446a37dc5'], + }), + ('readODS', '2.1.0', { + 'checksums': ['3f3e557ac7cadeda4759c51f866ce9a942cb21a2b3dd24e55a082fc7d300d7fe'], + }), + ('nortest', '1.0-4', { + 'checksums': ['a3850a048181d5d059c1e74903437569873b430c915b709808237d71fee5209f'], + }), + ('EnvStats', '2.8.1', { + 'checksums': ['12952b9eaa64b7bdbaaa5c6b7acb3aa1028ddfa4e5de7ddfea54f900c452d6a6'], + }), + ('outliers', '0.15', { + 'checksums': ['cc31d7f2faefd2c3a27f8ce78c7e67d3b321dcd6690292fad2468125e5e635fb'], + }), + ('gWidgets2', '1.0-9', { + 'checksums': ['d4d9ef7b2788efeb8209aa8dd610af4cd86286392fbdf9ea70bcfeafda95d4c5'], + }), + ('gWidgets2tcltk', '1.0-8', { + # need to run installation via xvfb-run to avoid problems on headless systems: + # no DISPLAY variable so Tk is not available + # [tcl] invalid command name "font" + 'preinstallopts': "xvfb-run ", + # skip 'import' check with library(gWidgets2tcltk), since it also fails on headless systems... + 'modulename': False, + 'checksums': ['10399cc636eeeb5484c3379970c37c56df10d979bf866a35b66d0c75b7222c0a'], + }), + ('mgsub', 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['bde8008b5fc8f0023bdd84b3a14a7425aecf1edcdf79480dac861895de4a9a9b'], + }), + ('svglite', '2.1.3', { + 'checksums': ['f0a8564e6f9127f4d1e05cf5a5f36b4e244aee0008e27473e504c63873ef0a54'], + }), + ('rARPACK', '0.11-0', { + 'checksums': ['c33401e2e31d272d485ce2ed22e7fe43ac641fd7c0a45a9b848d3ad60df1028a'], + }), + ('FKSUM', '1.0.1', { + 'checksums': ['6de23f5b7692f627b0b8e9575a612e77e166c16c28acab31d5ea0a27d7afe829'], + }), + ('warp', '0.2.1', { + 'checksums': ['020ad590de099661aa62b4d5e51499a2ac91c41c61db2dbc71c3f4a3df2c46be'], + }), + ('slider', '0.3.1', { + 'checksums': ['200a26795fadb2058e3976af7a697dde7f120645279cfe2580b8c0d6c0a429b0'], + }), + ('rsample', '1.2.0', { + 'checksums': ['e0c9b7060e0037f4213a5faad73f5910cf97bf93ecba93d35301cbc88cf45eed'], + }), + ('haldensify', '0.2.3', { + 'checksums': ['fc0ee1d5bce54520bad6a1ce1cce5074eead6c8573dc4ce502c48a244d7f341c'], + }), + ('Polychrome', '1.5.1', { + 'checksums': ['6fe7da62459d7b94b1a8516a4626971cf35b76331f46e36798b05d29aa00d143'], + }), + ('shinycssloaders', '1.0.0', { + 'checksums': ['744641836a4cede2bb47caff1b600bff2c3e450dfccd2af4fab0413a8ea87d64'], + }), + ('princurve', '2.1.6', { + 'checksums': ['0216332390eb27013b6ba62232782156dfc99ca640087fcaff53d2be9218f373'], + }), + ('ECOSolveR', '0.5.5', { + 'checksums': ['2594ed1602b2fe159cc9aff3475e9cba7c1927b496c3daeabc1c0d227943ecc7'], + }), + ('scs', '3.2.4', { + 'checksums': ['c3f39874bf4532fa8c2f2e2c41533ba4fe20b61cf6dfc6314407dc981621298f'], + }), + ('osqp', '0.6.3.2', { + 'checksums': ['18543b329a42be0f419dff4aa42f4401c2afb18f46276ce359853494dd803244'], + }), + ('CVXR', '1.0-11', { + 'checksums': ['e92a9638f35f4909e2a29c3b7106081e3dae7ff88b14bb6466b87fbdc80b972a'], + }), + ('tabletools', '0.1.0', { + 'source_urls': ['https://github.com/JMLuther/%(name)s/archive/'], + 'sources': [{'download_filename': 'cc961c5.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['667a4270456d28188734ce31411326130a94e085490ced84096c984789bb174a'], + }), + ('officer', '0.6.3', { + 'checksums': ['e51754029240d66fb1c8e6d524c63a275f6fafa19a22fef90d90c8ceb982777c'], + }), + ('gfonts', '0.2.0', { + 'checksums': ['72e2eead5280b45aadbbd9385971d65e9866fd659270b1c3c1eb98330f024aa6'], + }), + ('fontBitstreamVera', '0.1.1', { + 'checksums': ['3298b3dd95605bdda0c5fce5594c9bedde6aa63d89b216d5c83c6c092b6d375a'], + }), + ('fontLiberation', '0.1.0', { + 'checksums': ['acdea423e005873aa509e280074a3cef4796e4f7e9d77b3945d77b451ea039f0'], + }), + ('fontquiver', '0.2.1', { + 'checksums': ['95871814c2d55c03ee15a54e29aadfb840c791e1430f94127d9e1dc8608a6363'], + }), + ('gdtools', '0.3.5', { + 'checksums': ['8cb46da05b87440aadf6958baa37dd9b62d526c558622285146ea7cc4b51b894'], + }), + ('flextable', '0.9.4', { + 'checksums': ['55ad11660325cf470cedf532df774f99748583eb53c0162e2dede8e1c3539ab6'], + }), + ('ridge', '3.3', { + 'checksums': ['5c2daecf6f97aa099ef5fa54f8448518c4f2ed6e44dd29fc60621a70721c60f5'], + }), + ('ggdist', '3.3.1', { + 'checksums': ['6705e8a252701bc162bbbe26f7cbb3e95e93a11af6288456ab711f5d0c0df929'], + }), + ('svUnit', '1.0.6', { + 'checksums': ['263e6c03d6c2717dfd25b96d25f8019c9c98120de280a17224e0d79adba2d522'], + }), + ('arrayhelpers', '1.1-0', { + 'checksums': ['5fddd5dd4fb8237bcb24465ef823bc8715ba53e6e5fd7a716c31c48ec128340b'], + }), + ('tidybayes', '3.0.6', { + 'checksums': ['706044e17855a684a5ad1aeb582963dd3c7192a4a8ad0584358d0ea7c7aadb90'], + }), + ('spdep', '1.3-1', { + 'checksums': ['36062ccd094f9110a43cd51902c794242311fd23b861dde22c450446dce85396'], + }), + ('stringmagic', '1.0.0', { + 'checksums': ['8152c72a2ed70577fae1e569986d1d488ce2e6b21b8f0e080c0265806c08551a'], + }), + ('dreamerr', '1.4.0', { + 'checksums': ['3e5e4afd10623b6dac6bb9b8bf0480d41c7422884cfec2d9d9786414f9026a87'], + }), + ('fixest', '0.11.2', { + 'checksums': ['2dee113a0689e5c4dd842c451d35c9a94a5b37536f9484611a877c1ea10e2b65'], + }), + ('cmna', '1.0.5', { + 'checksums': ['7cf99880cb70e8fd0b022184167888b1ad32dca503e0250c1d552a84f0613898'], + }), + ('XBRL', '0.99.19.1', { + 'checksums': ['ad9ebb5431bdfecc38b8bf3b2552f1a048878a9ac02f5a9d71279b3b099a9757'], + }), + ('rhandsontable', '0.3.8', { + 'checksums': ['901ed9c59936f7fa52ad8db3111c8904ab962f9c74f1b6cd40f81683af35d21d'], + }), + ('missMDA', '1.19', { + 'checksums': ['f9675884829b2fef75237c335b21991d163674320e766523c71c7a853f95e65c'], + }), + ('gcmr', '1.0.3', { + 'checksums': ['75773d5119179f186467d33608e9ce1c030d0755dfd6ff196546884078e89754'], + }), +] + +modextrapaths = {'R_LIBS_SITE': ''} + +sanity_check_paths = { + 'files': [], + 'dirs': ['abind', 'base64', 'calibrate'], +} + +moduleclass = 'lang' diff --git a/467_scNanoGPS/R-bundle-test-gcmr.eb b/467_scNanoGPS/R-bundle-test-gcmr.eb new file mode 100644 index 00000000..ffdb160c --- /dev/null +++ b/467_scNanoGPS/R-bundle-test-gcmr.eb @@ -0,0 +1,71 @@ +easyblock = 'Bundle' + +name = 'R-bundle-CRAN-test-gcmr' +version = '2023.12' + +homepage = 'https://www.r-project.org/' +description = "Bundle of R packages from CRAN" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('R-bundle-CRAN', '2023.12'), +] + +# Some R extensions (mclust, quantreg, waveslim for example) require the math library (-lm) to avoid undefined symbols. +# Adding it to FLIBS makes sure it is present when needed. +preconfigopts = 'export FLIBS="$FLIBS -lm" && ' + +configopts = "--with-pic --enable-threads --enable-R-shlib" +# some recommended packages may fail in a parallel build (e.g. Matrix), and +# we're installing them anyway below +configopts += " --with-recommended-packages=no" + +exts_defaultclass = 'RPackage' + +exts_default_options = { + 'source_urls': [ + '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', +} + +# check whether correct version is installed in extension filter +# (some versions in this bundle may be newer than the ones provided by R) +local_ext_version_check = "pkgver = packageVersion('%(ext_name)s'); if (pkgver != '%(ext_version)s') " +local_stop_msg = "stop('%(ext_name)s %(ext_version)s not installed, found ', pkgver, ' instead')" +exts_filter = ("R -q --no-save", "%s { %s }" % (local_ext_version_check, local_stop_msg)) + +# the dbarts extension needs an additional compiler flag on Arm systems to prevent "incompatible types" errors +# cfr. https://github.com/vdorie/dbarts/issues/66 +if ARCH == 'aarch64': + local_dbarts_preinstallopts = 'sed -i "s|-c partition_neon.c|-flax-vector-conversions -c partition_neon.c|"' + local_dbarts_preinstallopts += ' src/misc/Makefile && ' +else: + local_dbarts_preinstallopts = '' + +# !! order of packages is important !! +# packages updated on 10th December 2023 +exts_list = [ + ('gcmr', '1.0.3', { + 'checksums': ['75773d5119179f186467d33608e9ce1c030d0755dfd6ff196546884078e89754'], + }), +] + +modextrapaths = {'R_LIBS_SITE': ''} + +sanity_check_paths = { + 'files': [], + 'dirs': ['gcmr'], +} + +# sanity_check_paths = { +# 'files': [], +# 'dirs': ['abind', 'base64', 'calibrate'], +# } + +sanity_check_commands = ['Rscript -e "library(gcmr)"'] + +moduleclass = 'lang' \ No newline at end of file diff --git a/467_scNanoGPS/annovar.eb b/467_scNanoGPS/annovar.eb new file mode 100644 index 00000000..724d59d4 --- /dev/null +++ b/467_scNanoGPS/annovar.eb @@ -0,0 +1,42 @@ +# J. Sassmannshausen /NHS/GSTT: toolchain updated to GCCcore-11.2 + +easyblock = 'Tarball' + +name = 'annovar' +version = '20200607' # version reported by `annotate_variation.pl -h` +versionsuffix = '-Perl-%(perlver)s' + +homepage = 'http://annovar.openbioinformatics.org/en/latest/' +description = """ANNOVAR is an efficient software tool to utilize update-to-date information +to functionally annotate genetic variants detected from diverse genomes (including human +genome hg18, hg19, hg38, as well as mouse, worm, fly, yeast and many others).""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +# Registration required for download +# http://www.openbioinformatics.org/annovar/annovar_download_form.php +# rename after download to %(name)s-%(version)s.tar.gz +sources = ['%(name)s-%(version)s.tar.gz'] +checksums = ['4061af3f2cc8f3d4d8187986c3d468a4b6ae145eec1858e85c7cd1059debb8ed'] +# www.openbioinformatics.org/annovar/download/0wgxr2rivp/annovar.latest.tar.gz +# http://www.openbioinformatics.org/annovar/download/0wgxr2rivp/annovar.latest.tar.gz +# http%3A%2F%2Fwww.openbioinformatics.org%2Fannovar%2Fdownload%2F0wgxR2rIVP%2Fannovar.latest.tar.gz +# https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.openbioinformatics.org%2Fannovar%2Fdownload%2F0wgxR2rIVP%2Fannovar.latest.tar.gz&data=05%7C02%7CPavel.Tomanek%40ugent.be%7C2bc2be1ddbd04f55603d08dd1845a0f8%7Cd7811cdeecef496c8f91a1786241b99c%7C1%7C0%7C638693409652782873%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=Q7QUiPCDxkpeaXGu8wqgNC8kxmTVd8dWerNLHPVBc8I%3D&reserved=0 +dependencies = [('Perl', '5.36.1'),] + +modextrapaths = { + 'PATH': '', +} + +sanity_check_paths = { + 'files': ["annotate_variation.pl", "coding_change.pl", "convert2annovar.pl", "retrieve_seq_from_fasta.pl", + "variants_reduction.pl", "table_annovar.pl"], + 'dirs': ["example", "humandb"], +} + +sanity_check_commands = [ + "annotate_variation.pl --help 2>&1 | grep 'Version: $Date: %s-%s-%s'" % (version[:4], version[4:6], version[6:]), + 'retrieve_seq_from_fasta.pl --help 2>&1 | grep "reformat sequences at specific genomic positions"', +] + +moduleclass = 'bio' diff --git a/467_scNanoGPS/bcftools.eb b/467_scNanoGPS/bcftools.eb new file mode 100644 index 00000000..f6fd731b --- /dev/null +++ b/467_scNanoGPS/bcftools.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'BCFtools' +version = '1.21' + +homepage = 'https://github.com/samtools/bcftools/' +description = """BCFtools is a program for variant calling and manipulating files in the Variant Call Format (VCF) +and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, +both uncompressed and BGZF-compressed.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://github.com/samtools/bcftools/releases/download/%(version)s/'] +sources = ['%(namelower)s-%(version)s.tar.bz2'] +checksums = ['528a4cc1d3555368db75a700b22a3c95da893fd1827f6d304716dfd45ea4e282'] + +builddependencies = [ + ('Autotools', '20220317'), +] +dependencies = [ + ('HTSlib', '1.18'), + ('GSL', '2.7'), + ('Perl', '5.36.1'), +] + +preconfigopts = 'autoheader && autoconf && ' +configopts = '--enable-libgsl --enable-perl-filters ' + +runtest = 'test' + +sanity_check_paths = { + 'files': ['bin/bcftools'], + 'dirs': ['libexec', 'share'], +} + +modextravars = {'BCFTOOLS_PLUGINS': '%(installdir)s/libexec/%(namelower)s'} + +moduleclass = 'bio' diff --git a/467_scNanoGPS/lifelines.eb b/467_scNanoGPS/lifelines.eb new file mode 100644 index 00000000..15c49466 --- /dev/null +++ b/467_scNanoGPS/lifelines.eb @@ -0,0 +1,43 @@ +easyblock = 'PythonBundle' + +name = 'lifelines' +version = '0.28.0' + +homepage = "https://lifelines.readthedocs.io/en/latest/" +description = """Lifelines is a complete survival analysis library, written in pure Python.""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +builddependencies = [('poetry', '1.5.1')] +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('matplotlib', '3.7.2'), + ('wrapt', '1.15.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('astor', '0.8.1', { + 'checksums': ['6a6effda93f4e1ce9f618779b2dd1d9d84f1e32812c23a29b3fff6fd7f63fa5e'], + }), + ('interface_meta', '1.3.0', { + 'checksums': ['8a4493f8bdb73fb9655dcd5115bc897e207319e36c8835f39c516a2d7e9d79a1'], + }), + ('autograd', '1.6.2', { + 'checksums': ['8731e08a0c4e389d8695a40072ada4512641c113b6cace8f4cfbe8eb7e9aedeb'], + }), + ('autograd-gamma', '0.5.0', { + 'checksums': ['f27abb7b8bb9cffc8badcbf59f3fe44a9db39e124ecacf1992b6d952934ac9c4'], + }), + ('formulaic', '1.0.1', { + 'checksums': ['64dd7992a7aa5bbceb1e40679d0f01fc6f0ba12b7d23d78094a88c2edc68fba1'], + }), + (name, version, { + 'checksums': ['eecf726453fd409c94fef8a521f8e593bcd09337f920fe885131f01cfe58b25e'], + }), +] + +moduleclass = 'bio' diff --git a/467_scNanoGPS/scNanoGPS.eb b/467_scNanoGPS/scNanoGPS.eb new file mode 100644 index 00000000..1c4b4664 --- /dev/null +++ b/467_scNanoGPS/scNanoGPS.eb @@ -0,0 +1,79 @@ +easyblock = 'PythonBundle' + +name = 'scNanoGPS' +version = '1.1' + +homepage = 'https://github.com/gaolabtools/scNanoGPS/' +description = "Single cell Nanopore sequencing data for Genotype and Phenotype." + +toolchain = {'name': 'foss', 'version': '2023a'} + +# DEPS: + # OK - biopython 1.79 + # ok - distance 0.1.3 + # OK - matplotlib 3.5.2 + # OK - pandas 1.4.2 + # OK - pysam 0.19.0 + # OK - seaborn 0.11.2 + # OK minimap2 + # OK Samtools + # OK UPDATED tabix + # OK SPOA + # OK SubRead featureCounts + # ok LIQA + # OK Longshot + # OK CREATED BFCtools + # !!! UPDATE ANNOVAR -> sources are not open -> no sources on hpc -> try to register and download -> 404 + # Optional: + # OK gffread + # Qualimap - not for 2023a + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('Biopython', '1.83'), + ('matplotlib', '3.7.2'), + ('Pysam', '0.22.0'), + ('Seaborn', '0.13.2'), + ('Perl', '5.36.1'), + ('minimap2', '2.26'), + ('SAMtools', '1.18'), + ('tabix', '0.2.6'), + ('spoa', '4.1.0'), + ('Subread', '2.0.6'), + ('Longshot', '1.0.0'), + ('BCFtools', '1.21'), + ('gffread', '0.12.7'), + # annovar +] + +use_pip = True + +exts_list = [ + ('liqa', '1.3.4', { + 'checksums': ['f8b2e6f0226d99f513d17be3758e6b3e2e9b7b40579f840d28737e827358850e'], + }), + ('Distance', '0.1.3', { + 'checksums': ['60807584f5b6003f5c521aa73f39f51f631de3be5cccc5a1d67166fcbf0d4551'], + }), + (name, version, { + 'source_urls': ['https://github.com/gaolabtools/scNanoGPS/archive/refs/tags/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['60cce1c771283b6d7a3639aa5744acfd6162306d95dd419ad3c265461fdda218'], + }), +] + +sanity_pip_check = True + +# sanity_check_paths = { +# 'files': ['bin/bonito'], +# 'dirs': ['lib/python%(pyshortver)s/site-packages'], +# } + +# sanity_check_commands = [ +# "bonito --help", +# "bonito download --help", +# ] + +moduleclass = 'bio' diff --git a/467_scNanoGPS/scNanoGPS_v2.eb b/467_scNanoGPS/scNanoGPS_v2.eb new file mode 100644 index 00000000..7be3f1e3 --- /dev/null +++ b/467_scNanoGPS/scNanoGPS_v2.eb @@ -0,0 +1,106 @@ +easyblock = 'Tarball' + +name = 'scNanoGPS' +version = '1.1' + +homepage = 'https://github.com/gaolabtools/scNanoGPS/' +description = "Single cell Nanopore sequencing data for Genotype and Phenotype." + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/gaolabtools/scNanoGPS/archive/refs/tags/'] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['60cce1c771283b6d7a3639aa5744acfd6162306d95dd419ad3c265461fdda218'] + +# DEPS: + # OK - biopython 1.79 + # ok - distance 0.1.3 + # OK - matplotlib 3.5.2 + # OK - pandas 1.4.2 + # OK - pysam 0.19.0 + # OK - seaborn 0.11.2 + # OK minimap2 + # OK Samtools + # OK UPDATED tabix + # OK SPOA + # OK SubRead featureCounts + # ok LIQA + # OK Longshot + # OK CREATED BFCtools + # !!! UPDATE ANNOVAR -> sources are not open -> no sources on hpc -> try to register and download -> 404 + # it is used in reporter_SNV.py + # Optional: + # OK gffread + # Qualimap - not for 2023a + # Liqa deps: + # OK Python + # OK Pysam + # OK Numpy + # OK Scipy + # OK UPDATED Lifelines - already lifelines in synthcity not used 2023a + # OK R + # ADD_TO_CRAN gcmr + # OK betareg + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('Biopython', '1.83'), + ('matplotlib', '3.7.2'), + ('Pysam', '0.22.0'), + ('Seaborn', '0.13.2'), + ('Perl', '5.36.1'), + ('minimap2', '2.26'), + ('SAMtools', '1.18'), + ('tabix', '0.2.6'), + ('spoa', '4.1.0'), + ('Subread', '2.0.6'), + ('Longshot', '1.0.0'), + ('BCFtools', '1.21'), + ('gffread', '0.12.7'), + ('lifelines', '0.28.0'), + ('R', '4.3.2'), + ('R-bundle-CRAN', '2023.12'), + # annovar +] + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'download_dep_fail': True, + 'use_pip': True, + # 'sanity_pip_check': False, +} + +exts_list = [ + ('liqa', '1.3.4', { + 'modulename': False, + 'checksums': ['f8b2e6f0226d99f513d17be3758e6b3e2e9b7b40579f840d28737e827358850e'], + }), + ('Distance', '0.1.3', { + 'checksums': ['60807584f5b6003f5c521aa73f39f51f631de3be5cccc5a1d67166fcbf0d4551'], + }), +] + +sanity_check_paths = { + 'files': ['bin/liqa'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "liqa -h", + "python -c 'import distance'", + "python other_utils/read_length_profiler.py -h", + "python scanner.py -h", + "python assigner.py -h", + "python curator.py -h ", + "python reporter_expression.py -h", + "python reporter_isoform.py -h", + "python reporter_SNV.py -h", + "python reporter_summary.py -h" +] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'bio' diff --git a/467_scNanoGPS/tabix.eb b/467_scNanoGPS/tabix.eb new file mode 100644 index 00000000..c27a6c1f --- /dev/null +++ b/467_scNanoGPS/tabix.eb @@ -0,0 +1,47 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# Author: Jens Timmerman, Ghent University +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# uploaded by J. Sassmannshausen +# updated to newer toolchain + +easyblock = 'MakeCp' + +name = 'tabix' +version = '0.2.6' + +homepage = 'https://samtools.sourceforge.net' +description = """ Generic indexer for TAB-delimited genome position files """ + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = [('https://sourceforge.net/projects/samtools/files/', 'download')] +sources = [SOURCE_TAR_BZ2] +checksums = ['e4066be7101bae83bec62bc2bc6917013f6c2875b66eb5055fbb013488d68b73'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [('zlib', '1.2.13')] + +buildopts = 'CC="$CC" CFLAGS="$CFLAGS -L$EBROOTZLIB/lib"' + +files_to_copy = [ + (["tabix", "bgzip", "tabix.py"], "bin"), + (["tabix.1"], "man/man1"), + (["libtabix.a"], "lib64"), + (["*.h"], "include"), + "example.gtf.gz", + "example.gtf.gz.tbi", + "NEWS", + "ChangeLog" +] + +sanity_check_paths = { + 'files': ["bin/tabix", "bin/bgzip", "bin/tabix.py", "lib/libtabix.a"], + 'dirs': ["include"], +} + +moduleclass = 'bio'