try another thing

Snakefile

@@ -83,27 +83,6 @@ def prepare_environment(stepname):
     return out, os.path.join(out, '%s.log' % stepname)
 
 
-def symlink_prokka():
-    # ## prokka by default will look databases where is located the binary.
-    # ## we have to softlink to put the binary somewhere and the databases somewhere else.
-    cmd = """
-    if [[ "{DBPATH}" = /* ]]
-    then
-        PP={DBPATH};
-    else
-        PP=$PWD/{DBPATH};
-    fi
-    DD=$(dirname $(which prokka))/../db
-    if [[ ! -L $DD ]]
-    then
-        echo "Softlinking $DD to $PP"
-        cd $(dirname $(which prokka))/.. && ln -s $PP db
-    fi
-    """
-    shell(cmd)
-
-symlink_prokka()
-
 # INCLUDES RULES
 include:
     "rules/Util.rules"

rules/Analysis/MGMT.rules

@@ -11,6 +11,20 @@ rule ANALYSIS_ANNOTATE:
         "%s/annotation/annotation.filt.gff" % AN_OUT
     shell:
         """
+        # ## prokka by default will look databases where is located the binary.
+        # ## we have to softlink to put the binary somewhere and the databases somewhere else.
+        if [[ "{DBPATH}" = /* ]]
+        then
+            PP={DBPATH};
+        else
+            PP=$PWD/{DBPATH};
+        fi
+        DD=$(dirname $(which prokka))/../db
+        if [[ ! -L $DD ]]
+        then
+            echo "Softlinking $DD to $PP"
+            cd $(dirname $(which prokka))/.. && ln -s $PP db
+        fi
         prokka --force --outdir {AN_OUT}/annotation --cpus {THREADS} --metagenome --norrna {input[0]} >> {log} 2>&1
         # Prokka gives a weird gff file with all the sequences. We need to write some small code to produce a file that
         # cleans up the output

rules/Util.rules

@@ -55,20 +55,6 @@ rule _DOWNLOAD_PROKKA_DATABASES:
         """
 
 
-
-rule _DOWNLOAD_TRIMMOMATIC_ADAPTERS:
-    output:
-        "{DBPATH}/adapters/adapters.done"
-    shell:
-        """
-        wget http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-Src-0.32.zip
-        unzip Trimmomatic-Src-0.32.zip
-        cp -r trimmomatic-0.32/adapters {DBPATH}
-        rm Trimmomatic-Src-0.32.zip && rm -rf trimmomatic-0.32
-        touch {output}
-        """
-
-
 rule _DOWNLOAD_LIBRARY_FILES:
     output:
         "lib/d3.min.js", "lib/d3pie.min.js", "lib/jquery-2.1.1.min.js"