#453 working truster - pre-PR versions

vscentrum · Nov 14, 2024 · 3801f9e · 3801f9e
1 parent 5f1ff32
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diff --git a/453_trusTEr/bamtofastq.eb b/453_trusTEr/bamtofastq.eb
@@ -10,11 +10,106 @@ toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
 
 source_urls = ['https://github.com/10XGenomics/bamtofastq/archive/refs/tags']
 sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}]
+checksums = [
+    {'bamtofastq-1.4.1.tar.gz': 'cebf968b0eff8911df65102e2be5884e6cd7312f1cb0aba6718bfc2d9407d543'},
+    {'addr2line-0.17.0.tar.gz': 'b9ecd88a8c8378ca913a680cd98f0f13ac67383d35993f86c90a70e3f137816b'},
+    {'adler-1.0.2.tar.gz': 'f26201604c87b1e01bd3d98f8d5d9a8fcbb815e8cedb41ffccbeb4bf593a35fe'},
+    {'aho-corasick-0.7.18.tar.gz': '1e37cfd5e7657ada45f742d6e99ca5788580b5c529dc78faf11ece6dc702656f'},
+    {'anyhow-1.0.53.tar.gz': '94a45b455c14666b85fc40a019e8ab9eb75e3a124e05494f5397122bc9eb06e0'},
+    {'autocfg-1.0.1.tar.gz': 'cdb031dd78e28731d87d56cc8ffef4a8f36ca26c38fe2de700543e627f8a464a'},
+    {'backtrace-0.3.63.tar.gz': '321629d8ba6513061f26707241fa9bc89524ff1cd7a915a97ef0c62c666ce1b6'},
+    {'bincode-1.3.3.tar.gz': 'b1f45e9417d87227c7a56d22e471c6206462cba514c7590c09aff4cf6d1ddcad'},
+    {'bio-types-0.12.0.tar.gz': '3f79d996fbffc59cbaeec4c831f9c1bbf6debdfadd9bb02ff4caf70507159c63'},
+    {'bitflags-1.3.2.tar.gz': 'bef38d45163c2f1dde094a7dfd33ccf595c92905c8f8f4fdc18d06fb1037718a'},
+    {'bstr-0.2.17.tar.gz': 'ba3569f383e8f1598449f1a423e72e99569137b47740b1da11ef19af3d5c3223'},
+    {'byteorder-1.4.3.tar.gz': '14c189c53d098945499cdfa7ecc63567cf3886b3332b312a5b4585d8d3a6a610'},
+    {'bzip2-sys-0.1.11+1.0.8.tar.gz': '736a955f3fa7875102d57c82b8cac37ec45224a07fd32d58f9f7a186b6cd4cdc'},
+    {'cc-1.0.71.tar.gz': '79c2681d6594606957bbb8631c4b90a7fcaaa72cdb714743a437b156d6a7eedd'},
+    {'cfg-if-1.0.0.tar.gz': 'baf1de4339761588bc0619e3cbc0120ee582ebb74b53b4efbf79117bd2da40fd'},
+    {'cmake-0.1.45.tar.gz': 'eb6210b637171dfba4cda12e579ac6dc73f5165ad56133e5d72ef3131f320855'},
+    {'crc32fast-1.2.1.tar.gz': '81156fece84ab6a9f2afdb109ce3ae577e42b1228441eded99bd77f627953b1a'},
+    {'crossbeam-channel-0.5.1.tar.gz': '06ed27e177f16d65f0f0c22a213e17c696ace5dd64b14258b52f9417ccb52db4'},
+    {'crossbeam-utils-0.8.5.tar.gz': 'd82cfc11ce7f2c3faef78d8a684447b40d503d9681acebed6cb728d45940c4db'},
+    {'csv-1.1.6.tar.gz': '22813a6dc45b335f9bade10bf7271dc477e81113e89eb251a0bc2a8a81c536e1'},
+    {'csv-core-0.1.10.tar.gz': '2b2466559f260f48ad25fe6317b3c8dac77b5bdb5763ac7d9d6103530663bc90'},
+    {'curl-sys-0.4.49+curl-7.79.1.tar.gz': 'e0f44960aea24a786a46907b8824ebc0e66ca06bf4e4978408c7499620343483'},
+    {'custom_derive-0.1.7.tar.gz': 'ef8ae57c4978a2acd8b869ce6b9ca1dfe817bff704c220209fdef2c0b75a01b9'},
+    {'derive-new-0.5.9.tar.gz': '3418329ca0ad70234b9735dc4ceed10af4df60eff9c8e7b06cb5e520d92c3535'},
+    {'docopt-1.1.1.tar.gz': '7f3f119846c823f9eafcf953a8f6ffb6ed69bf6240883261a7f13b634579a51f'},
+    {'either-1.6.1.tar.gz': 'e78d4f1cc4ae33bbfc157ed5d5a5ef3bc29227303d595861deb238fcec4e9457'},
+    {'fastrand-1.7.0.tar.gz': 'c3fcf0cee53519c866c09b5de1f6c56ff9d647101f81c1964fa632e148896cdf'},
+    {'flate2-1.0.22.tar.gz': '1e6988e897c1c9c485f43b47a529cef42fde0547f9d8d41a7062518f1d8fc53f'},
+    {'form_urlencoded-1.0.1.tar.gz': '5fc25a87fa4fd2094bffb06925852034d90a17f0d1e05197d4956d3555752191'},
+    {'fs-utils-1.1.4.tar.gz': '6fc7a9dc005c944c98a935e7fd626faf5bf7e5a609f94bc13e42fc4a02e52593'},
+    {'gimli-0.26.0.tar.gz': '81a03ce013ffccead76c11a15751231f777d9295b845cc1266ed4d34fcbd7977'},
+    {'glob-0.3.0.tar.gz': '9b919933a397b79c37e33b77bb2aa3dc8eb6e165ad809e58ff75bc7db2e34574'},
+    {'heck-0.3.3.tar.gz': '6d621efb26863f0e9924c6ac577e8275e5e6b77455db64ffa6c65c904e9e132c'},
+    {'hts-sys-2.0.2.tar.gz': '72c443906f4bac8b8cfe67e4e9d9ca83a454b70a092e1764133d19d5c5c7c1e2'},
+    {'idna-0.2.3.tar.gz': '418a0a6fab821475f634efe3ccc45c013f742efe03d853e8d3355d5cb850ecf8'},
+    {'ieee754-0.2.6.tar.gz': '9007da9cacbd3e6343da136e98b0d2df013f553d35bdec8b518f07bea768e19c'},
+    {'instant-0.1.12.tar.gz': '7a5bbe824c507c5da5956355e86a746d82e0e1464f65d862cc5e71da70e94b2c'},
+    {'itertools-0.10.3.tar.gz': 'a9a9d19fa1e79b6215ff29b9d6880b706147f16e9b1dbb1e4e5947b5b02bc5e3'},
+    {'itoa-0.4.8.tar.gz': 'b71991ff56294aa922b450139ee08b3bfc70982c6b2c7562771375cf73542dd4'},
+    {'jobserver-0.1.24.tar.gz': 'af25a77299a7f711a01975c35a6a424eb6862092cc2d6c72c4ed6cbc56dfc1fa'},
+    {'lazy_static-1.4.0.tar.gz': 'e2abad23fbc42b3700f2f279844dc832adb2b2eb069b2df918f455c4e18cc646'},
+    {'libc-0.2.103.tar.gz': 'dd8f7255a17a627354f321ef0055d63b898c6fb27eff628af4d1b66b7331edf6'},
+    {'libdeflate-sys-0.5.0.tar.gz': '21e39efa87b84db3e13ff4e2dfac1e57220abcbd7fe8ec44d238f7f4f787cc1f'},
+    {'libz-sys-1.1.3.tar.gz': 'de5435b8549c16d423ed0c03dbaafe57cf6c3344744f1242520d59c9d8ecec66'},
+    {'linear-map-1.2.0.tar.gz': 'bfae20f6b19ad527b550c223fddc3077a547fc70cda94b9b566575423fd303ee'},
+    {'log-0.4.14.tar.gz': '51b9bbe6c47d51fc3e1a9b945965946b4c44142ab8792c50835a980d362c2710'},
+    {'lz4-1.23.2.tar.gz': 'aac20ed6991e01bf6a2e68cc73df2b389707403662a8ba89f68511fb340f724c'},
+    {'lz4-sys-1.9.2.tar.gz': 'dca79aa95d8b3226213ad454d328369853be3a1382d89532a854f4d69640acae'},
+    {'lzma-sys-0.1.17.tar.gz': 'bdb4b7c3eddad11d3af9e86c487607d2d2442d185d848575365c4856ba96d619'},
+    {'matches-0.1.9.tar.gz': 'a3e378b66a060d48947b590737b30a1be76706c8dd7b8ba0f2fe3989c68a853f'},
+    {'memchr-2.4.1.tar.gz': '308cc39be01b73d0d18f82a0e7b2a3df85245f84af96fdddc5d202d27e47b86a'},
+    {'min-max-heap-1.3.0.tar.gz': '2687e6cf9c00f48e9284cf9fd15f2ef341d03cc7743abf9df4c5f07fdee50b18'},
+    {'miniz_oxide-0.4.4.tar.gz': 'a92518e98c078586bc6c934028adcca4c92a53d6a958196de835170a01d84e4b'},
+    {'newtype_derive-0.1.6.tar.gz': 'ac8cd24d9f185bb7223958d8c1ff7a961b74b1953fd05dba7cc568a63b3861ec'},
+    {'object-0.27.1.tar.gz': '67ac1d3f9a1d3616fd9a60c8d74296f22406a238b6a72f5cc1e6f314df4ffbf9'},
+    {'openssl-src-111.16.0+1.1.1l.tar.gz': '7ab2173f69416cf3ec12debb5823d244127d23a9b127d5a5189aa97c5fa2859f'},
+    {'openssl-sys-0.9.67.tar.gz': '69df2d8dfc6ce3aaf44b40dec6f487d5a886516cf6879c49e98e0710f310a058'},
+    {'percent-encoding-2.1.0.tar.gz': 'd4fd5641d01c8f18a23da7b6fe29298ff4b55afcccdf78973b24cf3175fee32e'},
+    {'pkg-config-0.3.20.tar.gz': '7c9b1041b4387893b91ee6746cddfc28516aff326a3519fb2adf820932c5e6cb'},
+    {'proc-macro2-1.0.29.tar.gz': 'b9f5105d4fdaab20335ca9565e106a5d9b82b6219b5ba735731124ac6711d23d'},
+    {'quick-error-1.2.3.tar.gz': 'a1d01941d82fa2ab50be1e79e6714289dd7cde78eba4c074bc5a4374f650dfe0'},
+    {'quote-1.0.10.tar.gz': '38bc8cc6a5f2e3655e0899c1b848643b2562f853f114bfec7be120678e3ace05'},
+    {'redox_syscall-0.2.10.tar.gz': '8383f39639269cde97d255a32bdb68c047337295414940c68bdd30c2e13203ff'},
+    {'regex-1.5.4.tar.gz': 'd07a8629359eb56f1e2fb1652bb04212c072a87ba68546a04065d525673ac461'},
+    {'regex-automata-0.1.10.tar.gz': '6c230d73fb8d8c1b9c0b3135c5142a8acee3a0558fb8db5cf1cb65f8d7862132'},
+    {'regex-syntax-0.6.25.tar.gz': 'f497285884f3fcff424ffc933e56d7cbca511def0c9831a7f9b5f6153e3cc89b'},
+    {'remove_dir_all-0.5.3.tar.gz': '3acd125665422973a33ac9d3dd2df85edad0f4ae9b00dafb1a05e43a9f5ef8e7'},
+    {'rust-htslib-0.38.2.tar.gz': '2aca6626496389f6e015e25433b85e2895ad3644b44de91167d847bf2d8c1a1c'},
+    {'rustc-demangle-0.1.21.tar.gz': '7ef03e0a2b150c7a90d01faf6254c9c48a41e95fb2a8c2ac1c6f0d2b9aefc342'},
+    {'rustc_version-0.1.7.tar.gz': 'c5f5376ea5e30ce23c03eb77cbe4962b988deead10910c372b226388b594c084'},
+    {'ryu-1.0.5.tar.gz': '71d301d4193d031abdd79ff7e3dd721168a9572ef3fe51a1517aba235bd8f86e'},
+    {'semver-0.1.20.tar.gz': 'd4f410fedcf71af0345d7607d246e7ad15faaadd49d240ee3b24e5dc21a820ac'},
+    {'serde-1.0.135.tar.gz': '2cf9235533494ea2ddcdb794665461814781c53f19d87b76e571a1c35acbad2b'},
+    {'serde_bytes-0.11.5.tar.gz': '16ae07dd2f88a366f15bd0632ba725227018c69a1c8550a927324f8eb8368bb9'},
+    {'serde_derive-1.0.135.tar.gz': '8dcde03d87d4c973c04be249e7d8f0b35db1c848c487bd43032808e59dd8328d'},
+    {'shardio-0.8.2.tar.gz': '669590a22936d55698744e4096bc46fc8f935f492fe86b2f09cbdbb6d937b65a'},
+    {'strsim-0.10.0.tar.gz': '73473c0e59e6d5812c5dfe2a064a6444949f089e20eec9a2e5506596494e4623'},
+    {'strum_macros-0.20.1.tar.gz': 'ee8bc6b87a5112aeeab1f4a9f7ab634fe6cbefc4850006df31267f4cfb9e3149'},
+    {'syn-1.0.80.tar.gz': 'd010a1623fbd906d51d650a9916aaefc05ffa0e4053ff7fe601167f3e715d194'},
+    {'tempfile-3.3.0.tar.gz': '5cdb1ef4eaeeaddc8fbd371e5017057064af0911902ef36b39801f67cc6d79e4'},
+    {'thiserror-1.0.29.tar.gz': '602eca064b2d83369e2b2f34b09c70b605402801927c65c11071ac911d299b88'},
+    {'thiserror-impl-1.0.29.tar.gz': 'bad553cc2c78e8de258400763a647e80e6d1b31ee237275d756f6836d204494c'},
+    {'tinyvec-1.5.0.tar.gz': 'f83b2a3d4d9091d0abd7eba4dc2710b1718583bd4d8992e2190720ea38f391f7'},
+    {'tinyvec_macros-0.1.0.tar.gz': 'cda74da7e1a664f795bb1f8a87ec406fb89a02522cf6e50620d016add6dbbf5c'},
+    {'unicode-bidi-0.3.7.tar.gz': '1a01404663e3db436ed2746d9fefef640d868edae3cceb81c3b8d5732fda678f'},
+    {'unicode-normalization-0.1.19.tar.gz': 'd54590932941a9e9266f0832deed84ebe1bf2e4c9e4a3554d393d18f5e854bf9'},
+    {'unicode-segmentation-1.8.0.tar.gz': '8895849a949e7845e06bd6dc1aa51731a103c42707010a5b591c0038fb73385b'},
+    {'unicode-xid-0.2.2.tar.gz': '8ccb82d61f80a663efe1f787a51b16b5a51e3314d6ac365b08639f52387b33f3'},
+    {'url-2.2.2.tar.gz': 'a507c383b2d33b5fc35d1861e77e6b383d158b2da5e14fe51b83dfedf6fd578c'},
+    {'vcpkg-0.2.15.tar.gz': 'accd4ea62f7bb7a82fe23066fb0957d48ef677f6eeb8215f372f52e48bb32426'},
+    {'winapi-0.3.9.tar.gz': '5c839a674fcd7a98952e593242ea400abe93992746761e38641405d28b00f419'},
+    {'winapi-i686-pc-windows-gnu-0.4.0.tar.gz': 'ac3b87c63620426dd9b991e5ce0329eff545bccbbb34f3be09ff6fb6ab51b7b6'},
+    {'winapi-x86_64-pc-windows-gnu-0.4.0.tar.gz': '712e227841d057c1ee1cd2fb22fa7e5a5461ae8e48fa2ca79ec42cfc1931183f'},
+]
 
 builddependencies = [
     ('binutils', '2.40'),
     ('Rust', '1.75.0'),
-    # ('CMake', '3.20.1'),
+    ('CMake', '3.26.3'),
 ]
 
 dependencies = [('bzip2', '1.0.8')]
@@ -122,3 +217,13 @@ sanity_check_paths = {
 sanity_check_commands = ["%(namelower)s --help"]
 
 moduleclass = 'bio'
+
+# E1: 
+    # error: failed to run custom build command for `libz-sys v1.1.3`
+    # note: To improve backtraces for build dependencies, set the CARGO_PROFILE_RELEASE_BUILD_OVERRIDE_DEBUG=true environmene to enable debug information generation.
+    # Caused by:
+    #   process didn't exit successfully: `/tmp/vsc47063/easybuild/build/bamtofastq/1.4.1/GCCcore-12.3.0/bamtofastq-1.4.1/taase/build/libz-sys-f6d7ace8052e76bc/build-script-build` (exit status: 101)
+    #   --- stdout
+    #   cargo:rerun-if-env-changed=LIBZ_SYS_STATIC
+    #   cargo:rerun-if-changed=build.rs
+    #   running: cd "/tmp/vsc47063/easybuild/build/bamtofastq/1.4.1/GCCcore-12.3.0/bamtofastq-1.4.1/target/release/build/libe1e9b86e652b3/out/build" && CMAKE_PREFIX_PATH="/apps/gent/RHEL8/cascadelake-ib/software/bzip2/1.0.8-GCCcore-1ps/gent/RHEL8/cascadelake-ib/software/Rust/1.75.0-GCCcore-12.3.0:/apps/gent/RHEL8/cascadelake-ib/software/Ope/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.40-GCCcore-12.3.0:/apps/gent/RHEL8/cascadelake-ib/softwar2.13-GCCcore-12.3.0:/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/12.3.0" "cmake" "/tmp/vsc47063/easybuildmtofastq/1.4.1/GCCcore-12.3.0/easybuild_vendor/libz-sys-1.1.3/src/zlib-ng" "-DBUILD_SHARED_LIBS=OFF" "-DZLIB_ake-ampere-ib/software/.locks/_scratch_gent_vo_001_gvo00117_easybuild_RHEL8_cascadelake-ampere-ib_software_bamtofastq_1.4.1-GCCcore-12.3.0.lock...
diff --git a/453_trusTEr/subset-bam_binary.eb b/453_trusTEr/subset-bam_binary.eb
@@ -0,0 +1,26 @@
+easyblock = 'Binary'
+
+name = 'subset-bam'
+version = '1.1.0'
+
+homepage = 'https://github.com/10XGenomics/subset-bam'
+description = """subset-bam is a tool to subset a 10x Genomics BAM file based on a tag, 
+most commonly the cell barcode tag."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+source_urls = ['https://github.com/10XGenomics/subset-bam/releases/download/v%(version)s/']
+
+sources = [{'download_filename': 'subset-bam_linux', 'filename': name}]
+checksums = ['05496ea56d52becdb7972528af0a486be1d52c1749e35bea9ae4c41215ed0a1b']
+
+sanity_check_paths = {
+    'dirs': [],
+    'files': [name],
+}
+
+sanity_check_commands = ["%(name)s --help"]
+
+modextrapaths = {'PATH': ''}
+
+moduleclass = 'bio'
diff --git a/453_trusTEr/truster.eb b/453_trusTEr/truster.eb
@@ -1,13 +1,18 @@
-easyblock = 'PythonBundle'
+easyblock = 'PythonPackage'
 
 name = 'trusTEr'
-version = '0.1.1'
+version = '0.1.1-20241025'
+local_commit = '6358eef'
 
 homepage = 'https://github.com/raquelgarza/truster'
 description = """Takes fastq files from 10x single cell RNA sequencing, clusters cells using Seurat,
 and can be used to produce read count matrices in a cluster level.
 You can also quantify reads per cluster having predefined clusters."""
 
+source_urls = ['https://github.com/raquelgarza/truster/archive/']
+sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}]
+checksums = ['ef6f454a73f545e5f90a28a80d388afb763a43ac1256f3c182bf947728b4e39a']
+
 toolchain = {'name': 'foss', 'version': '2023a'}
 
 #DEPS:
@@ -16,9 +21,9 @@ toolchain = {'name': 'foss', 'version': '2023a'}
     # OK Seurat
     # OK UPDATE - TEtranscripts
     # OK STAR aligner
-    # UPDATE - subset-bam
-    # UPDATE - bamtofastq
-    # Velocyto
+    # OK UPDATE - subset-bam
+    # OK UPDATE - bamtofastq
+    # OK Velocyto
 
 # builddependencies = [
 #     ('hatchling', '1.18.0'),
@@ -28,24 +33,26 @@ toolchain = {'name': 'foss', 'version': '2023a'}
 # ]
 dependencies = [
     ('Python', '3.11.3'),
-    # ('Python-bundle-PyPI', '2023.06'),
     ('SciPy-bundle', '2023.07'),
     ('CellRanger', '8.0.1', '', SYSTEM),
     ('R', '4.3.2'),
     ('R-bundle-CRAN', '2023.12'),
     ('Seurat', '5.1.0', '-R-%(rver)s'),
     ('STAR', '2.7.11a'),
     ('velocyto', '0.17.17'),
-    ('TEtranscripts' '2.2.3'),
+    ('TEtranscripts','2.2.3'),
+    ('bamtofastq','1.4.1'),
+    ('subset-bam', '1.1.0'),
 ]
 
 use_pip = True
+download_dep_fail = True
 
-exts_list = [
-    ('truster', version, {
-        'checksums': ['36081b7aac1988566b0d42278f77671faabe17725006e56865b0ec5f7374e185'],
-    }),
-]
+# exts_list = [
+#     ('truster', version, {
+#         'checksums': ['36081b7aac1988566b0d42278f77671faabe17725006e56865b0ec5f7374e185'],
+#     }),
+# ]
 
     # (name, version, {
     #     # delete cmake and ninja deps to let pip check pass