From 74350f0604d792599b93763796bc498b65fe9436 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Tue, 19 Nov 2024 16:41:03 +0100 Subject: [PATCH] #453 done - cleanup --- 453_trusTEr/bamtofastq.eb | 220 -------------- 453_trusTEr/old_subset-bam.eb | 311 ------------------- 453_trusTEr/old_subset-bam_11.3.0.eb | 311 ------------------- 453_trusTEr/subset-bam.eb | 429 --------------------------- 453_trusTEr/subset-bam_binary.eb | 24 -- 453_trusTEr/subset-bam_master.eb | 309 ------------------- 453_trusTEr/tetranscripts.eb | 42 --- 453_trusTEr/truster.eb | 36 --- 8 files changed, 1682 deletions(-) delete mode 100644 453_trusTEr/bamtofastq.eb delete mode 100644 453_trusTEr/old_subset-bam.eb delete mode 100644 453_trusTEr/old_subset-bam_11.3.0.eb delete mode 100644 453_trusTEr/subset-bam.eb delete mode 100644 453_trusTEr/subset-bam_binary.eb delete mode 100644 453_trusTEr/subset-bam_master.eb delete mode 100644 453_trusTEr/tetranscripts.eb delete mode 100644 453_trusTEr/truster.eb diff --git a/453_trusTEr/bamtofastq.eb b/453_trusTEr/bamtofastq.eb deleted file mode 100644 index 8759374..0000000 --- a/453_trusTEr/bamtofastq.eb +++ /dev/null @@ -1,220 +0,0 @@ -easyblock = 'Cargo' - -name = 'bamtofastq' -version = '1.4.1' - -homepage = 'https://github.com/10XGenomics/bamtofastq' -description = """Convert 10x BAM files to the original FASTQs compatible with 10x pipelines.""" - -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}] - -builddependencies = [ - ('binutils', '2.40'), - ('Rust', '1.75.0'), - ('CMake', '3.26.3'), -] - -dependencies = [('bzip2', '1.0.8')] - -crates = [ - ('addr2line', '0.17.0'), - ('adler', '1.0.2'), - ('aho-corasick', '0.7.18'), - ('anyhow', '1.0.53'), - ('autocfg', '1.0.1'), - ('backtrace', '0.3.63'), - ('bincode', '1.3.3'), - ('bio-types', '0.12.0'), - ('bitflags', '1.3.2'), - ('bstr', '0.2.17'), - ('byteorder', '1.4.3'), - ('bzip2-sys', '0.1.11+1.0.8'), - ('cc', '1.0.71'), - ('cfg-if', '1.0.0'), - ('cmake', '0.1.45'), - ('crc32fast', '1.2.1'), - ('crossbeam-channel', '0.5.1'), - 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{'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'}, -] - -moduleclass = 'bio' diff --git a/453_trusTEr/old_subset-bam.eb b/453_trusTEr/old_subset-bam.eb deleted file mode 100644 index d61b28c..0000000 --- a/453_trusTEr/old_subset-bam.eb +++ /dev/null @@ -1,311 +0,0 @@ -# Author: J. Sassmannshausen (Imperial College London/UK) - -easyblock = 'Cargo' - -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': '12.2.0'} - -crates = [ - ('addr2line', '0.12.1'), - ('adler32', '1.1.0'), - ('aho-corasick', '0.6.10'), - ('aho-corasick', '0.7.10'), - ('ansi_term', '0.11.0'), - ('arrayref', '0.3.6'), - ('arrayvec', '0.5.1'), - ('atty', '0.2.14'), - ('autocfg', '1.0.0'), - ('backtrace', '0.3.49'), - ('base64', '0.11.0'), - ('bindgen', '0.36.1'), - ('bitflags', '0.9.1'), - ('bitflags', '1.2.1'), - ('blake2b_simd', '0.5.10'), - ('bstr', '0.2.13'), - ('byteorder', '1.3.4'), - ('cc', '1.0.54'), - ('cexpr', '0.2.3'), - ('cfg-if', '0.1.10'), - ('chrono', '0.4.11'), - ('clang-sys', '0.22.0'), - ('clap', '2.33.1'), - ('constant_time_eq', '0.1.5'), - ('crossbeam-deque', '0.7.3'), - ('crossbeam-epoch', '0.8.2'), - ('crossbeam-queue', '0.2.3'), - ('crossbeam-utils', '0.7.2'), - ('csv', '1.1.3'), - ('csv-core', '0.1.10'), - ('custom_derive', '0.1.7'), - ('data-encoding', '2.2.1'), - ('dirs', '1.0.5'), - ('either', '1.5.3'), - ('env_logger', '0.5.13'), - ('faccess', '0.2.3'), - ('failure', '0.1.8'), - ('failure_derive', '0.1.8'), - ('fs-utils', '1.1.4'), - ('getrandom', '0.1.14'), - ('gimli', '0.21.0'), - ('glob', '0.2.11'), - ('hermit-abi', '0.1.14'), - ('human-panic', '1.0.3'), - ('humantime', '1.3.0'), - ('idna', '0.1.5'), - ('ieee754', '0.2.6'), - ('itertools', '0.6.5'), - ('itoa', '0.4.6'), - ('lazy_static', '0.2.11'), - ('lazy_static', '1.4.0'), - ('libc', '0.2.71'), - ('libloading', '0.5.2'), - ('linear-map', '1.2.0'), - ('log', '0.4.8'), - ('matches', '0.1.8'), - ('maybe-uninit', '2.0.0'), - ('memchr', '1.0.2'), - ('memchr', '2.3.3'), - ('memoffset', '0.5.4'), - ('miniz_oxide', '0.3.7'), - ('newtype_derive', '0.1.6'), - ('nom', '3.2.1'), - ('num-integer', '0.1.43'), - 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{'winapi-x86_64-pc-windows-gnu-0.4.0.tar.gz': '712e227841d057c1ee1cd2fb22fa7e5a5461ae8e48fa2ca79ec42cfc1931183f'}, -] - -# GCC-11.3.0 + Rust-1.65.0 works -# GCC-12.2.0 + Rust-1.65.0 NOT work -builddependencies = [ - ('binutils', '2.39'), - ('Rust', '1.65.0'), - ('Clang', '16.0.4'), -] - -dependencies = [ - ('bzip2', '1.0.8'), -] - -# It looks like we need to specify this as else it will not work. -buildopts = '-Z unstable-options ' -testopts = '-Z unstable-options ' -installopts = '-Z unstable-options ' - -sanity_check_paths = { - 'files': ['bin/subset-bam'], - 'dirs': [], -} - -sanity_check_commands = ["subset-bam --help"] - -moduleclass = 'bio' diff --git a/453_trusTEr/old_subset-bam_11.3.0.eb b/453_trusTEr/old_subset-bam_11.3.0.eb deleted file mode 100644 index 4f97ed2..0000000 --- a/453_trusTEr/old_subset-bam_11.3.0.eb +++ /dev/null @@ -1,311 +0,0 @@ -# Author: J. Sassmannshausen (Imperial College London/UK) - -easyblock = 'Cargo' - -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': '11.3.0'} - -crates = [ - ('addr2line', '0.12.1'), - ('adler32', '1.1.0'), - ('aho-corasick', '0.6.10'), - ('aho-corasick', '0.7.10'), - ('ansi_term', '0.11.0'), - ('arrayref', '0.3.6'), - ('arrayvec', '0.5.1'), - ('atty', '0.2.14'), - ('autocfg', '1.0.0'), - ('backtrace', '0.3.49'), - ('base64', '0.11.0'), - ('bindgen', '0.36.1'), - ('bitflags', '0.9.1'), - ('bitflags', '1.2.1'), - ('blake2b_simd', '0.5.10'), - ('bstr', '0.2.13'), - ('byteorder', '1.3.4'), - ('cc', '1.0.54'), - ('cexpr', '0.2.3'), - ('cfg-if', '0.1.10'), - ('chrono', '0.4.11'), - ('clang-sys', '0.22.0'), - ('clap', '2.33.1'), - ('constant_time_eq', '0.1.5'), - ('crossbeam-deque', '0.7.3'), - ('crossbeam-epoch', '0.8.2'), - ('crossbeam-queue', '0.2.3'), - ('crossbeam-utils', '0.7.2'), - ('csv', '1.1.3'), - ('csv-core', '0.1.10'), - ('custom_derive', '0.1.7'), - ('data-encoding', '2.2.1'), - ('dirs', '1.0.5'), - ('either', '1.5.3'), - ('env_logger', '0.5.13'), - ('faccess', '0.2.3'), - ('failure', '0.1.8'), - ('failure_derive', '0.1.8'), - ('fs-utils', '1.1.4'), - ('getrandom', '0.1.14'), - ('gimli', '0.21.0'), - ('glob', '0.2.11'), - ('hermit-abi', '0.1.14'), - ('human-panic', '1.0.3'), - ('humantime', '1.3.0'), - ('idna', '0.1.5'), - ('ieee754', '0.2.6'), - ('itertools', '0.6.5'), - ('itoa', '0.4.6'), - ('lazy_static', '0.2.11'), - ('lazy_static', '1.4.0'), - ('libc', '0.2.71'), - ('libloading', '0.5.2'), - ('linear-map', '1.2.0'), - ('log', '0.4.8'), - ('matches', '0.1.8'), - ('maybe-uninit', '2.0.0'), - ('memchr', '1.0.2'), - ('memchr', '2.3.3'), - ('memoffset', '0.5.4'), - ('miniz_oxide', '0.3.7'), - ('newtype_derive', '0.1.6'), - ('nom', '3.2.1'), - ('num-integer', '0.1.43'), - 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('strsim', '0.8.0'), - ('syn', '1.0.31'), - ('synstructure', '0.12.4'), - ('tempfile', '3.1.0'), - ('term', '0.5.2'), - ('termcolor', '1.1.0'), - ('terminal_size', '0.1.12'), - ('textwrap', '0.11.0'), - ('thread_local', '0.3.6'), - ('thread_local', '1.0.1'), - ('time', '0.1.43'), - ('tinyvec', '0.3.3'), - ('toml', '0.5.6'), - ('ucd-util', '0.1.8'), - ('unicode-bidi', '0.3.4'), - ('unicode-normalization', '0.1.13'), - ('unicode-width', '0.1.7'), - ('unicode-xid', '0.1.0'), - ('unicode-xid', '0.2.0'), - ('untrusted', '0.6.2'), - ('url', '1.7.2'), - ('utf8-ranges', '1.0.4'), - ('uuid', '0.8.1'), - ('vec_map', '0.8.2'), - ('wasi', '0.9.0+wasi-snapshot-preview1'), - ('which', '1.0.5'), - ('winapi', '0.3.8'), - ('winapi-i686-pc-windows-gnu', '0.4.0'), - ('winapi-util', '0.1.5'), - ('winapi-x86_64-pc-windows-gnu', '0.4.0'), -] - -source_urls = ['https://github.com/10XGenomics/subset-bam/archive/'] -sources = ['v%(version)s.tar.gz'] -checksums = [ - {'v1.1.0.tar.gz': 'af7e384dbacbebe55c6173ec8e52b2cebc95e69b922114003668575550b7227f'}, - 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{'winapi-x86_64-pc-windows-gnu-0.4.0.tar.gz': '712e227841d057c1ee1cd2fb22fa7e5a5461ae8e48fa2ca79ec42cfc1931183f'}, -] - -# GCC-11.3.0 + Rust-1.65.0 works -# GCC-12.2.0 + Rust-1.65.0 NOT work -builddependencies = [ - ('binutils', '2.38'), - ('Rust', '1.65.0'), - ('Clang', '15.0.5'), -] - -dependencies = [ - ('bzip2', '1.0.8'), -] - -# It looks like we need to specify this as else it will not work. -buildopts = '-Z unstable-options ' -testopts = '-Z unstable-options ' -installopts = '-Z unstable-options ' - -sanity_check_paths = { - 'files': ['bin/subset-bam'], - 'dirs': [], -} - -sanity_check_commands = ["subset-bam --help"] - -moduleclass = 'bio' diff --git a/453_trusTEr/subset-bam.eb b/453_trusTEr/subset-bam.eb deleted file mode 100644 index 37a8a3a..0000000 --- a/453_trusTEr/subset-bam.eb +++ /dev/null @@ -1,429 +0,0 @@ -# Author: J. Sassmannshausen (Imperial College London/UK) -# Update: Pavel Tománek (Inuits) - -easyblock = 'Cargo' - -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/archive/'] -sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] -checksums = [ - {'subset-bam-1.1.0.tar.gz': 'af7e384dbacbebe55c6173ec8e52b2cebc95e69b922114003668575550b7227f'}, - {'addr2line-0.24.2.tar.gz': 'dfbe277e56a376000877090da837660b4427aad530e3028d44e0bffe4f89a1c1'}, - {'adler2-2.0.0.tar.gz': '512761e0bb2578dd7380c6baaa0f4ce03e84f95e960231d1dec8bf4d7d6e2627'}, - {'aho-corasick-0.6.10.tar.gz': '81ce3d38065e618af2d7b77e10c5ad9a069859b4be3c2250f674af3840d9c8a5'}, - {'aho-corasick-1.1.3.tar.gz': '8e60d3430d3a69478ad0993f19238d2df97c507009a52b3c10addcd7f6bcb916'}, - 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('wasm-bindgen-backend', '0.2.95'), - ('wasm-bindgen-macro', '0.2.95'), - ('wasm-bindgen-macro-support', '0.2.95'), - ('wasm-bindgen-shared', '0.2.95'), - ('which', '1.0.5'), - ('winapi', '0.3.9'), - ('winapi-i686-pc-windows-gnu', '0.4.0'), - ('winapi-util', '0.1.9'), - ('winapi-x86_64-pc-windows-gnu', '0.4.0'), - ('windows-core', '0.52.0'), - ('windows-sys', '0.52.0'), - ('windows-sys', '0.59.0'), - ('windows-targets', '0.52.6'), - ('windows_aarch64_gnullvm', '0.52.6'), - ('windows_aarch64_msvc', '0.52.6'), - ('windows_i686_gnu', '0.52.6'), - ('windows_i686_gnullvm', '0.52.6'), - ('windows_i686_msvc', '0.52.6'), - ('windows_x86_64_gnu', '0.52.6'), - ('windows_x86_64_gnullvm', '0.52.6'), - ('windows_x86_64_msvc', '0.52.6'), -] - -prebuildopts = "rm Cargo.lock && " # not working - -# It looks like we need to specify this as else it will not work. -buildopts = '-Z unstable-options ' -testopts = '-Z unstable-options ' -installopts = '-Z unstable-options ' - -sanity_check_paths = { - 'files': ['bin/subset-bam'], - 'dirs': [], -} - -sanity_check_commands = ["subset-bam --help"] - -moduleclass = 'bio' - -# E1: - # -> delete Cargo.lock -> another error: - # error[E0283]: type annotations needed - # --> /tmp/vsc47063/easybuild/build/subsetbam/1.1.0/GCCcore-12.3.0/easybuild_vendor/ring-0.14.6/build.rs:475:52 - # | - # 475 | let _ = c.flag("-Wl,--gc-sections".into()); - # | ---- ^^^^ - # | | - # | required by a bound introduced by this call - # | - # = note: multiple `impl`s satisfying `_: AsRef` found in the following crates: `cc`, `std`: - # - impl AsRef for OsStr; - # - impl AsRef for OsString; - # - impl AsRef for Path; - # - impl AsRef for PathBuf; - # - impl AsRef for String; - # - impl AsRef for str; - # - impl AsRef for windows_registry::Env; - # note: required by a bound in `Build::flag` - # --> /tmp/vsc47063/easybuild/build/subsetbam/1.1.0/GCCcore-12.3.0/easybuild_vendor/cc-1.2.1/src/lib.rs:537:39 - # | - # 537 | pub fn flag(&mut self, flag: impl AsRef) -> &mut Build { - # | ^^^^^^^^^^^^ required by this bound in `Build::flag` - # help: try using a fully qualified path to specify the expected types - # | - # 475 | let _ = c.flag(<&str as Into>::into("-Wl,--gc-sections")); - # | ++++++++++++++++++++++++ ~ - - # For more information about this error, try `rustc --explain E0283`. - # error: could not compile `ring` (build script) due to previous error - # -> build failed (with new Cargo.lock) error: - # == 2024-11-14 12:22:54,368 build_log.py:171 ERROR EasyBuild crashed with an error (at easybuild/easybuild-framework/easybuild/base/exceptions.py:126 in __init__): cmd " cargo build --profile=release --tests -j 8 -Z unstable-options " exited with exit code 101 and output: - # error: failed to select a version for the requirement `clap = "*"` (locked to 2.33.1) - # candidate versions found which didn't match: 4.5.21, 2.34.0 - # location searched: directory source `/tmp/vsc47063/easybuild/build/subsetbam/1.1.0/GCCcore-12.3.0/easybuild_vendor` (which is replacing registry `crates-io`) - # required by package `subset-bam v1.1.0 (/tmp/vsc47063/easybuild/build/subsetbam/1.1.0/GCCcore-12.3.0/subset-bam-1.1.0)` - # perhaps a crate was updated and forgotten to be re-vendored? - # As a reminder, you're using offline mode (--offline) which can sometimes cause surprising resolution failures, if this error is too confusing you may wish to retry without the offline flag. \ No newline at end of file diff --git a/453_trusTEr/subset-bam_binary.eb b/453_trusTEr/subset-bam_binary.eb deleted file mode 100644 index f9e6778..0000000 --- a/453_trusTEr/subset-bam_binary.eb +++ /dev/null @@ -1,24 +0,0 @@ -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 = SYSTEM - -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"] - -moduleclass = 'bio' diff --git a/453_trusTEr/subset-bam_master.eb b/453_trusTEr/subset-bam_master.eb deleted file mode 100644 index 8bd069a..0000000 --- a/453_trusTEr/subset-bam_master.eb +++ /dev/null @@ -1,309 +0,0 @@ -# Author: J. Sassmannshausen (Imperial College London/UK) -# Update: Pavel Tománek (Inuits) - -easyblock = 'Cargo' - -name = 'subset-bam' -version = '1.1.0-20230907' -local_commit = 'c135329' - -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/archive/'] -sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] -checksums = [ - {'subset-bam-1.1.0-20230907.tar.gz': 'a50acbb049199e5578a7c7e457c6cdeeffa8d76591cc8466cbd4c8c9ca7f308d'}, - {'addr2line-0.12.1.tar.gz': 'a49806b9dadc843c61e7c97e72490ad7f7220ae249012fbda9ad0609457c0543'}, - {'adler32-1.1.0.tar.gz': '567b077b825e468cc974f0020d4082ee6e03132512f207ef1a02fd5d00d1f32d'}, - {'aho-corasick-0.6.10.tar.gz': '81ce3d38065e618af2d7b77e10c5ad9a069859b4be3c2250f674af3840d9c8a5'}, - 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('adler32', '1.1.0'), - ('aho-corasick', '0.6.10'), - ('aho-corasick', '0.7.10'), - ('ansi_term', '0.11.0'), - ('arrayref', '0.3.6'), - ('arrayvec', '0.5.1'), - ('atty', '0.2.14'), - ('autocfg', '1.0.0'), - ('backtrace', '0.3.49'), - ('base64', '0.11.0'), - ('bindgen', '0.36.1'), - ('bitflags', '0.9.1'), - ('bitflags', '1.2.1'), - ('blake2b_simd', '0.5.10'), - ('bstr', '0.2.13'), - ('byteorder', '1.3.4'), - ('cc', '1.0.54'), - ('cexpr', '0.2.3'), - ('cfg-if', '0.1.10'), - ('chrono', '0.4.11'), - ('clang-sys', '0.22.0'), - ('clap', '2.33.1'), - ('constant_time_eq', '0.1.5'), - ('crossbeam-deque', '0.7.3'), - ('crossbeam-epoch', '0.8.2'), - ('crossbeam-queue', '0.2.3'), - ('crossbeam-utils', '0.7.2'), - ('csv', '1.1.3'), - ('csv-core', '0.1.10'), - ('custom_derive', '0.1.7'), - ('data-encoding', '2.2.1'), - ('dirs', '1.0.5'), - ('either', '1.5.3'), - ('env_logger', '0.5.13'), - ('faccess', '0.2.4'), - ('failure', '0.1.8'), - ('failure_derive', '0.1.8'), - ('fs-utils', '1.1.4'), - ('getrandom', '0.1.14'), - ('gimli', '0.21.0'), - ('glob', '0.2.11'), - ('hermit-abi', '0.1.14'), - ('human-panic', '1.0.3'), - ('humantime', '1.3.0'), - ('idna', '0.1.5'), - ('ieee754', '0.2.6'), - ('itertools', '0.6.5'), - ('itoa', '0.4.6'), - ('lazy_static', '0.2.11'), - ('lazy_static', '1.4.0'), - ('libc', '0.2.71'), - ('libloading', '0.5.2'), - ('linear-map', '1.2.0'), - ('log', '0.4.19'), - ('matches', '0.1.8'), - ('maybe-uninit', '2.0.0'), - ('memchr', '1.0.2'), - ('memchr', '2.3.3'), - ('memoffset', '0.5.4'), - ('miniz_oxide', '0.3.7'), - ('newtype_derive', '0.1.6'), - ('nom', '3.2.1'), - ('num-integer', '0.1.43'), - ('num-traits', '0.2.12'), - ('num_cpus', '1.13.0'), - ('object', '0.20.0'), - ('os_type', '2.2.0'), - ('peeking_take_while', '0.1.2'), - ('percent-encoding', '1.0.1'), - ('ppv-lite86', '0.2.8'), - ('proc-macro2', '0.3.5'), - ('proc-macro2', '1.0.18'), - ('quick-error', '1.2.3'), - ('quote', '0.5.2'), - ('quote', '1.0.7'), - ('rand', '0.7.3'), - ('rand_chacha', '0.2.2'), - ('rand_core', '0.5.1'), - ('rand_hc', '0.2.0'), - ('rayon', '1.3.1'), - ('rayon-core', '1.7.1'), - ('redox_syscall', '0.1.56'), - ('redox_users', '0.3.4'), - ('regex', '0.2.11'), - ('regex', '1.3.9'), - ('regex-automata', '0.1.9'), - ('regex-syntax', '0.5.6'), - ('regex-syntax', '0.6.18'), - ('remove_dir_all', '0.5.3'), - ('ring', '0.14.6'), - ('rust-argon2', '0.7.0'), - ('rust-htslib', '0.20.0'), - ('rustc-demangle', '0.1.16'), - ('rustc_version', '0.1.7'), - ('ryu', '1.0.5'), - ('scopeguard', '1.1.0'), - ('semver', '0.1.20'), - ('serde', '1.0.113'), - ('serde_derive', '1.0.113'), - ('simplelog', '0.5.3'), - ('spin', '0.5.2'), - ('strsim', '0.8.0'), - ('syn', '1.0.31'), - ('synstructure', '0.12.4'), - ('tempfile', '3.1.0'), - ('term', '0.5.2'), - ('termcolor', '1.1.0'), - ('terminal_size', '0.1.12'), - ('textwrap', '0.11.0'), - ('thread_local', '0.3.6'), - ('thread_local', '1.0.1'), - ('time', '0.1.43'), - ('tinyvec', '0.3.3'), - ('toml', '0.5.6'), - ('ucd-util', '0.1.8'), - ('unicode-bidi', '0.3.4'), - ('unicode-normalization', '0.1.13'), - ('unicode-width', '0.1.7'), - ('unicode-xid', '0.1.0'), - ('unicode-xid', '0.2.0'), - ('untrusted', '0.6.2'), - ('url', '1.7.2'), - ('utf8-ranges', '1.0.4'), - ('uuid', '0.8.1'), - ('vec_map', '0.8.2'), - ('wasi', '0.9.0+wasi-snapshot-preview1'), - ('which', '1.0.5'), - ('winapi', '0.3.8'), - ('winapi-i686-pc-windows-gnu', '0.4.0'), - ('winapi-util', '0.1.5'), - ('winapi-x86_64-pc-windows-gnu', '0.4.0'), -] - -# It looks like we need to specify this as else it will not work. -# buildopts = '-Z unstable-options ' -# testopts = '-Z unstable-options ' -# installopts = '-Z unstable-options ' - -sanity_check_paths = { - 'files': ['bin/subset-bam'], - 'dirs': [], -} - -sanity_check_commands = ["subset-bam --help"] - -moduleclass = 'bio' diff --git a/453_trusTEr/tetranscripts.eb b/453_trusTEr/tetranscripts.eb deleted file mode 100644 index ab7aa30..0000000 --- a/453_trusTEr/tetranscripts.eb +++ /dev/null @@ -1,42 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'TEtranscripts' -version = '2.2.3' - -homepage = 'https://github.com/mhammell-laboratory/TEtranscripts' -description = """TEtranscripts and TEcount takes RNA-seq (and similar data) and annotates reads -to both genes & transposable elements. -TEtranscripts then performs differential analysis using DESeq2.""" - -sources = [SOURCE_TAR_GZ] -checksums = ['e53577e8e73e41c6495fb819977e3e537bbeac7b2fa1635029201a37ee0bf7b8'] - -toolchain = {'name': 'foss', 'version': '2023a'} - -dependencies = [ - ('Python', '3.11.3'), - ('Pysam', '0.22.0'), - ('R', '4.3.2'), - ('R-bundle-Bioconductor', '3.18', '-R-%(rver)s'), -] - -use_pip = True -download_dep_fail = True - -options = {'modulename': 'TEToolkit'} - -fix_python_shebang_for = ['bin/*'] - -sanity_check_paths = { - 'files': ['bin/TEtranscripts', 'bin/TEcount'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -sanity_check_commands = [ - 'TEtranscripts --version', - 'TEcount --version', -] - -sanity_pip_check = True - -moduleclass = 'bio' diff --git a/453_trusTEr/truster.eb b/453_trusTEr/truster.eb deleted file mode 100644 index 3bea110..0000000 --- a/453_trusTEr/truster.eb +++ /dev/null @@ -1,36 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'trusTEr' -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'} - -dependencies = [ - ('Python', '3.11.3'), - ('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'), - ('bamtofastq', '1.4.1'), - ('subset-bam', '1.1.0', '', SYSTEM), -] - -use_pip = True -download_dep_fail = True -sanity_pip_check = True - -moduleclass = 'bio'