setup rules: minor changes; operams setup (issue #43)

workflow/rules/setup.smk

@@ -3,8 +3,7 @@ rule install_casc:
     output:
         os.path.join(MOD_DIR, "casc/bin/casc")
     log:
-        out="logs/casc_install.out.log",
-        err="logs/casc_install.err.log"
+        "logs/setup.casc.log"
     params:
         path=os.path.join(MOD_DIR, "casc")
     conda:
@@ -12,19 +11,14 @@ rule install_casc:
     message:
         "Setup: install CASC"
     shell:
-        "(cd {params.path} && "
-        "perl Makefile.PL PREFIX=\"$(realpath .)\" && "
-        "make && "
-        "make test && "
-        "make install) 2> {log.err} > {log.out}"
+        "(cd {params.path} && perl Makefile.PL PREFIX=\"$(realpath .)\" && make && make test && make install) &> {log}"
 
 # MinCED
 rule install_minced:
     output:
         os.path.join(MOD_DIR, "minced/minced.jar")
     log:
-        out="logs/minced_install.out.log",
-        err="logs/minced_install.err.log"
+        "logs/setup.minced.log"
     params:
         path=os.path.join(MOD_DIR, "minced")
     conda:
@@ -32,9 +26,22 @@ rule install_minced:
     message:
         "Setup: install MinCED"
     shell:
-        "(cd {params.path} && "
-        "make && "
-        "make test) 2> {log.err} > {log.out}"
+        "(cd {params.path} && make && make test) &> {log}"
+
+# OPERA-MS
+rule install_operams:
+    output:
+        os.path.join(MOD_DIR, "operams/OPERA-MS.pl")
+    log:
+        "logs/setup.operams.log"
+    params:
+        path=os.path.join(MOD_DIR, "operams")
+    conda:
+        os.path.join(ENV_DIR, "operams.yaml")
+    message:
+        "Setup: install OPERA-MS"
+    shell:
+        "(cd ${params.path} && make && perl utils/install_perl_module.pl && perl OPERA-MS.pl check-dependency) &> {log}"
 
 # Download RGI data
 rule download_rgi_db:
@@ -42,8 +49,7 @@ rule download_rgi_db:
         archive=temp(os.path.join(DB_DIR, "rgi/card-data.tar.bz2")),
         json=os.path.join(DB_DIR, "rgi/card.json")
     log:
-        out="logs/rgi_db.out.log",
-        err="logs/rgi_db.err.log"
+        "logs/setup.rgi.db.log"
     params:
         db_url=config["rgi"]["db_url"]
     message:
@@ -52,7 +58,7 @@ rule download_rgi_db:
         "(date && "
         "wget -O {output.archive} {params.db_url} --no-check-certificate && "
         "tar -C $(dirname {output.archive}) -xvf {output.archive} && "
-        "date) 2> {log.err} > {log.out}"
+        "date) &> {log}"
 
 # Setup RGI: load required DB
 # NOTE: to make sure that the same DB is used for all targets
@@ -62,23 +68,21 @@ rule setup_rgi_db:
     output:
         "status/rgi_setup.done"
     log:
-        out="logs/rgi_setup.out.log",
-        err="logs/rgi_setup.err.log"
+        "logs/setup.rgi.setup.log"
     conda:
         os.path.join(ENV_DIR, "rgi.yaml")
     message:
         "Setup: load RGI DB"
     shell:
-        "(rgi clean --local && "
-        "rgi load --card_json {input} --local && "
-        "rgi database --version --local) 2> {log.err} > {log.out} && "
-        "touch {output}"
+        "(rgi clean --local && rgi load --card_json {input} --local && rgi database --version --local) &> {log} && touch {output}"
 
 # Reference genome FASTA for bbmap to remove host contamination
 rule setup_bbmap_host_ref:
     output:
         os.path.join(DB_DIR, "{bname}.fasta")
+    log:
+        "logs/setup.bbmap.hostref.log"
     params:
         url=lambda wildcards, output: config["bbmap"]["host_refs"][wildcards.bname]
     shell:
-        "wget -O {output}.gz {params.url} && gzip -d {output}.gz"
+        "(wget -O {output}.gz {params.url} && gzip -d {output}.gz) &> {log}"