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Laura Denies
PathoFact
Commits
8facd498
Commit
8facd498
authored
Apr 21, 2020
by
Valentina Galata
Browse files
HMMER: added YAML, changed path on config.yaml, added conda in rules (issue
#22
)
parent
e18bd311
Changes
4
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config.yaml
View file @
8facd498
...
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@@ -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"
#################
...
...
envs/HMMER.yaml
0 → 100644
View file @
8facd498
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
rules/Toxin/Toxin.snk
View file @
8facd498
...
...
@@ -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:
...
...
rules/Virulence/Virulence.snk
View file @
8facd498
...
...
@@ -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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