Gembs #10109
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| #!/bin/bash | ||
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| #instead of installing software from submodules, let them be dependencies | ||
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| $PYTHON setup.py install --minimal --single-version-externally-managed --record=record.txt | ||
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| {% set version = "conda_v2" %} | ||
| {% set sha256 = "1ead3f20a36a40c0737ec58c2e783b9c1cb6a9de0317c0009964d1b164c598a0" %} | ||
| {% set bcftoolsversion = "1.8" %} | ||
| {% set bcftoolssha256 = "4acbfd691f137742e0be63d09f516434f0faf617a5c60f466140e0677915fced"%} | ||
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| package: | ||
| name: gembs | ||
| version: {{ version }} | ||
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| source: | ||
| - url: https://github.com/karl616/gemBS/archive/{{ version }}.tar.gz | ||
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There was a problem hiding this comment. is this a fork from the original repo ? is the original one not being maintained anymore ? There was a problem hiding this comment. This is leftovers from testing, connected to the funky version above. Should be changed. |
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| sha256: {{ sha256 }} | ||
| - url: https://github.com/samtools/bcftools/releases/download/{{ bcftoolsversion }}/bcftools-{{ bcftoolsversion }}.tar.bz2 | ||
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There was a problem hiding this comment. is the bcftools source files being used ? its not obvious from the build.sh. There was a problem hiding this comment. Yes, there is a custom compiled bcftools version installed to the python library location. It makes use of the plugin system of bcftools. There was a problem hiding this comment. but is the script going to use this one if its there ? There was a problem hiding this comment. The script will prioritize the instance installed to the library folder, with a fall-back to the main-path. The download process is part of a Makefile. If the folder is already populated by conda, the download step during installation will be skipped. So yes, the file referred here is the one being used. |
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| sha256: {{ bcftoolssha256 }} | ||
| folder: tools/bcftools | ||
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| build: | ||
| number: 0 | ||
| skip: True # [py27] | ||
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| requirements: | ||
| build: | ||
| - {{ compiler('c') }} | ||
| host: | ||
| - python >=3.0 | ||
| - zlib | ||
| - bzip2 | ||
| - xz | ||
| - htslib =1.8 | ||
| - matplotlib | ||
| - multiprocess | ||
| - curl | ||
| - wget | ||
| run: | ||
| - python >=3.0 | ||
| - zlib | ||
| - bzip2 | ||
| - xz | ||
| - pigz | ||
| - htslib =1.8 | ||
| - matplotlib | ||
| - multiprocess | ||
| - samtools =1.8 | ||
| - gem3-mapper =3.6.1 | ||
| - bs_call =2.02 | ||
| - curl | ||
| - wget | ||
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| test: | ||
| commands: | ||
| - gemBS | ||
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| about: | ||
| home: https://github.com/heathsc/gemBS | ||
| license: GPL-3.0 | ||
| license_file: LICENSE.md | ||
| summary: gemBS is a bioinformatics pipeline designed for high throughput analysis of DNA methylation from Whole Genome Bisulfite Sequencing data (WGBS). | ||
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| extra: | ||
| identifiers: | ||
| - doi:10.1101/201988 | ||
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it would be best if the version of the package reflected the actual version of the software.
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Thank you for pointing this out. I'll have to ask for an up to date release. I'll definitely change this.