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" ...@@ -31,7 +31,7 @@ signalp: "/path/to/signalp-4.1/signalp"
############ ############
# Define path to HMM # Define path to HMM
hmmscan_tool: "/path/to/hmmer-3.2.1/src/hmmsearch" hmmscan_tool: "hmmsearch"
hmm_file: "databases/toxins/combined_Toxin.hmm" 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: ...@@ -17,6 +17,8 @@ rule run_HMM:
"Run HMM scan on {input[1]} to generate {output}" "Run HMM scan on {input[1]} to generate {output}"
params: params:
outdir="{OUTDIR}" outdir="{OUTDIR}"
conda:
"../../envs/HMMER.yaml"
threads: threads:
1 1
shell: shell:
......
...@@ -17,6 +17,8 @@ rule run_HMM_vir: ...@@ -17,6 +17,8 @@ rule run_HMM_vir:
"Run HMM scan on {input[1]} to generate {output}" "Run HMM scan on {input[1]} to generate {output}"
params: params:
outdir="{OUTDIR}" outdir="{OUTDIR}"
conda:
"../../envs/HMMER.yaml"
threads: threads:
12 12
shell: shell:
......
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