Maker: update 2.31.10 + add support for mpi (#2149)

Maker: update 2.31.10 + add support for mpi
galaxyproject · May 3, 2019 · 4141a68 · 4141a68
2 parents de12f17 + dfcd9ba
commit 4141a68
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Showing 2 changed files with 5 additions and 5 deletions.
diff --git a/tools/maker/macros.xml b/tools/maker/macros.xml
@@ -6,7 +6,7 @@
             <yield />
         </requirements>
     </xml>
-    <token name="@VERSION@">2.31.9</token>
+    <token name="@VERSION@">2.31.10</token>
 
     <xml name="citations">
         <citations>

diff --git a/tools/maker/maker.xml b/tools/maker/maker.xml
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="maker" name="Maker" profile="16.04" version="@VERSION@.1">
+<tool id="maker" name="Maker" profile="16.04" version="@VERSION@">
     <description>genome annotation pipeline</description>
     <macros>
         <import>macros.xml</import>
@@ -18,7 +18,7 @@
 
         &&
 
-        sed "s/cpus=/cpus=\${GALAXY_SLOTS:-4}/g" '$ctl' > maker_opts.ctl
+        cp '$ctl' maker_opts.ctl
 
         &&
 
@@ -35,7 +35,7 @@
             export AUGUSTUS_CONFIG_PATH=`pwd`/augustus_dir/ &&
         #end if
 
-        maker maker_opts.ctl maker_bopts.ctl maker_exe.ctl
+        mpiexec -n \${GALAXY_SLOTS:-4} maker maker_opts.ctl maker_bopts.ctl maker_exe.ctl < /dev/null
 
         &&
 
@@ -192,7 +192,7 @@ other_gff= # extra features to pass-through to final MAKER generated GFF3 file
 
 #-----External Application Behavior Options
 alt_peptide=${advanced.alt_peptide} # amino acid used to replace non-standard amino acids in BLAST databases
-cpus= # max number of cpus to use in BLAST and RepeatMasker (not for MPI, leave 1 when using MPI)
+cpus=1 # max number of cpus to use in BLAST and RepeatMasker (not for MPI, leave 1 when using MPI)
 
 #-----MAKER Behavior Options
 max_dna_len=${advanced.max_dna_len} # length for dividing up contigs into chunks (increases/decreases memory usage)