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Commit b785aac9 authored by Thomas  BIGOT's avatar Thomas BIGOT
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updated requirements

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...@@ -4,10 +4,15 @@ This respository contains scrits to translate and cluster the original nucleic s ...@@ -4,10 +4,15 @@ This respository contains scrits to translate and cluster the original nucleic s
## Requirements ## Requirements
* snakemake 5.x: <https://bitbucket.org/snakemake/snakemake> or `pip install snakemake` Here are the requirements and the used versions.
* golden 3.4.1: <https://projets.pasteur.fr/projects/golden/wiki>
* silix 1.2.6: <http://lbbe.univ-lyon1.fr/-SiLiX-> * snakemake 5.4.0 <https://bitbucket.org/snakemake/snakemake> or `pip install snakemake`
* blast+ <https://blast.ncbi.nlm.nih.gov> * golden 3.4.1 <https://projets.pasteur.fr/projects/golden/wiki>
* silix 1.2.6 <http://lbbe.univ-lyon1.fr/-SiLiX->
* blast+ 2.6.0 <https://blast.ncbi.nlm.nih.gov>
* Python 3.6 <https://www.python.org>
* hmmer 3.2 <http://hmmer.org>
* mafft 7.023 <https://mafft.cbrc.jp/alignment/software/>
## Usage ## Usage
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...@@ -55,7 +55,7 @@ rule Profiles_hmmbuild: ...@@ -55,7 +55,7 @@ rule Profiles_hmmbuild:
hmm="hmm/{part}.hmm", hmm="hmm/{part}.hmm",
log="hmm/{part}.log" log="hmm/{part}.log"
run: run:
shell("module load hmmer/3.1b2 ; hmmbuild --informat afa -n {wildcards.part} -o {output.log} {output.hmm} {input}") shell("module load hmmer/3.2 ; hmmbuild --informat afa -n {wildcards.part} -o {output.log} {output.hmm} {input}")
rule Profiles_align: rule Profiles_align:
input: input:
......
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