# HG changeset patch
# User iuc
# Date 1556884254 14400
# Node ID d3a2072d87459ac4c5e63e493f8209161680d382
# Parent 73a79dec987b0476653184c78c2d154da7064776
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 4141a68e0ce1cf6a24f721dce31b81b56f249088
diff -r 73a79dec987b -r d3a2072d8745 macros.xml
--- a/macros.xml Sun Jul 01 16:12:18 2018 -0400
+++ b/macros.xml Fri May 03 07:50:54 2019 -0400
@@ -6,7 +6,7 @@
- 2.31.9
+ 2.31.10
diff -r 73a79dec987b -r d3a2072d8745 maker.xml
--- a/maker.xml Sun Jul 01 16:12:18 2018 -0400
+++ b/maker.xml Fri May 03 07:50:54 2019 -0400
@@ -1,5 +1,5 @@
-
+
genome annotation pipeline
macros.xml
@@ -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 @@
#-----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)