Lumpy-express dependencies added #14215
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Added hexdump-, sambamba- and samblaster dependencies under run and increased the build number to 4.
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I am running the biocontainer of lumpy, specifically lumpy-express (quay.io/biocontainers/lumpy-sv:0.2.14a--hdfb72b2_2) in a wdl workflow. I get the following error: This is the code in line 15 from (https://github.com/arq5x/lumpy-sv/blob/master/scripts/lumpyexpress ) Furthermore, lumpy-express requires sambamba and samblaster https://github.com/arq5x/lumpy-sv#installation |
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@druvus Thank you! |
tfursten
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Mar 31, 2019
* add mtsv recipe trigger rebuild Update build.sh Update conda_build_config.yaml Update meta.yaml change python pinning * update adVNTR to 1.3.0 (#14209) * add adVNTR * fix linux error for adVNTR * add numpy to adVNTR requirements * add numpy include dirs for cythonize * Update advntr to 1.1.0 * Update advntr to 1.1.0 * update advntr to 1.1.1 * update adVNTR to 1.2.0 * update sha256 for adVNTR-1.2.0 * fix build script for adVNTR-1.2.0 * fix adVNTR-1.2.0 * update advntr and its requirements * update advntr -- pysam and htslib versions * skip py37 * force python version to be less than 3.7 * fix noarch problem * exclude python 3.7 * fix a typo * try another approach to exclude py37 * Update meta.yaml * Bump toulligqc (#14221) * Lumpy-express dependencies added (#14215) Added hexdump-, sambamba- and samblaster dependencies under run and increased the build number to 4. * Update clever-toolkit and distribute a shared library with kmc (#14224) * Update clever-toolkit and distribute a shared library with kmc * skip KMC on OSX, it uses gcc-specific headers * Nanopolish bioconda update (#14218) * bump nanopolish recipe to version 0.11.1 * bump nanopolish version to 0.11.1; update build number * remove libgcc @paultsw do you think its possible to remove the gcc execption for OSX already? * Irida uploader (#14118) :information_source: Bioconda has finished the [GCC7 migration](#13578). If you are dealing with C/C++ or Python package it can be that you need to rebuild other dependent packages. [Bioconda utils - update-pinning](https://bioconda.github.io/updating.html#updating-recipes-for-a-pinning-change) will assist you with that. If you have any questions please use [issue 13578](#13578). ---------------- * [x] I have read the [guidelines for bioconda recipes](https://bioconda.github.io/guidelines.html). * [x] This PR adds a new recipe. * [x] AFAIK, this recipe **is directly relevant to the biological sciences** (otherwise, please submit to the more general purpose [conda-forge channel](https://conda-forge.org/docs/)). * [ ] This PR updates an existing recipe. * [ ] This PR does something else (explain below). * change requirement versions to match v2.1.2 and bumped version (#14231) * Update duphold to 0.1.2 (#14232) * Add recipe for Augustus 3.3.2 (#14219) * Add recipe for Augustus 3.3.2 * Add recipe for GapFiller 2.1.1. (#14234) * Bumped GATK4 version (#14222) :information_source: Bioconda has finished the [GCC7 migration](#13578). If you are dealing with C/C++ or Python package it can be that you need to rebuild other dependent packages. [Bioconda utils - update-pinning](https://bioconda.github.io/updating.html#updating-recipes-for-a-pinning-change) will assist you with that. If you have any questions please use [issue 13578](#13578). ---------------- * [X] I have read the [guidelines for bioconda recipes](https://bioconda.github.io/guidelines.html). * [] This PR adds a new recipe. * [X] AFAIK, this recipe **is directly relevant to the biological sciences** (otherwise, please submit to the more general purpose [conda-forge channel](https://conda-forge.org/docs/)). * [X] This PR updates an existing recipe. * [ ] This PR does something else (explain below). * add orca to nanocomp, make noarch (#14228) add mtsv recipe trigger rebuild Update build.sh Update conda_build_config.yaml Update meta.yaml change python pinning add maintainer fix copy of mtsv-db-build fix binary list pip install pip install remove setuptools rm imports test test setuptools pinning remove mtsv-db test bump build * change build * move binaries to prefix/bin * force recheck
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Added hexdump-, sambamba- and samblaster dependencies under run and increased the build number to 4.
ℹ️
Bioconda has finished the GCC7 migration. If you are dealing with C/C++ or Python package it can be that you need to rebuild other dependent packages. Bioconda utils - update-pinning will assist you with that. If you have any questions please use issue 13578.