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

config.yaml

@@ -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

+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

@@ -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

@@ -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: