Commit 8facd498 authored by Valentina Galata's avatar Valentina Galata
Browse files

HMMER: added YAML, changed path on config.yaml, added conda in rules (issue #22)

parent e18bd311
......@@ -31,7 +31,7 @@ signalp: "/path/to/signalp-4.1/signalp"
############
# Define path to HMM
hmmscan_tool: "/path/to/hmmer-3.2.1/src/hmmsearch"
hmmscan_tool: "hmmsearch"
hmm_file: "databases/toxins/combined_Toxin.hmm"
#################
......
channels:
- bioconda
- conda-forge
- defaults
dependencies:
- _libgcc_mutex=0.1=conda_forge
- _openmp_mutex=4.5=0_gnu
- hmmer=3.2.1=he1b5a44_2
- libgcc-ng=9.2.0=h24d8f2e_2
- libgomp=9.2.0=h24d8f2e_2
- libstdcxx-ng=9.2.0=hdf63c60_2
......@@ -17,6 +17,8 @@ rule run_HMM:
"Run HMM scan on {input[1]} to generate {output}"
params:
outdir="{OUTDIR}"
conda:
"../../envs/HMMER.yaml"
threads:
1
shell:
......
......@@ -17,6 +17,8 @@ rule run_HMM_vir:
"Run HMM scan on {input[1]} to generate {output}"
params:
outdir="{OUTDIR}"
conda:
"../../envs/HMMER.yaml"
threads:
12
shell:
......
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