# HG changeset patch
# User iuc
# Date 1609197454 0
# Node ID e06aa22b2e64ddc1bde0eafb7b26d9b5d664e6f1
# Parent 804af884eef0581b85e48ceffc2dfb6c71701603
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 5bef07276e14b38cca31ef724d0b4d2f55809715"
diff -r 804af884eef0 -r e06aa22b2e64 macros.xml
--- a/macros.xml Thu Oct 10 02:55:17 2019 -0400
+++ b/macros.xml Mon Dec 28 23:17:34 2020 +0000
@@ -6,7 +6,7 @@
- 2.31.10
+ 2.31.11
diff -r 804af884eef0 -r e06aa22b2e64 maker.xml
--- a/maker.xml Thu Oct 10 02:55:17 2019 -0400
+++ b/maker.xml Mon Dec 28 23:17:34 2020 +0000
@@ -1,19 +1,23 @@
-
+
genome annotation pipeline
macros.xml
&2 ; exit 1 ; fi &&
+
+ LIBDIR=\$(dirname "\$RM_PATH")/../share/RepeatMasker/Libraries &&
+ #if $repeat_masking.repeat_source.source_type == "dfam_up":
+ mkdir lib/ &&
+ ln -s '${repeat_masking.repeat_source.dfam_lib}' lib/RepeatMaskerLib.h5 &&
+ LIBDIR=\$(pwd)/lib &&
#end if
+ export LIBDIR &&
+
maker -CTL
&&
@@ -35,7 +39,12 @@
export AUGUSTUS_CONFIG_PATH=`pwd`/augustus_dir/ &&
#end if
- mpiexec -n \${GALAXY_SLOTS:-4} maker --ignore_nfs_tmp maker_opts.ctl maker_bopts.ctl maker_exe.ctl < /dev/null
+ MPI_CMD="mpiexec -n \${GALAXY_SLOTS:-4}" &&
+ if [ "\$MAKER_NO_MPI" != "1" ]; then
+ MPI_CMD="";
+ fi &&
+
+ \${MPI_CMD} maker --ignore_nfs_tmp maker_opts.ctl maker_bopts.ctl maker_exe.ctl < /dev/null
&&
@@ -112,7 +121,7 @@
#end if
#-----Repeat Masking (leave values blank to skip repeat masking)
-#if $repeat_masking.repeat_source.source_type == 'repbase'
+#if $repeat_masking.repeat_source.source_type == 'dfam'
#if $repeat_masking.repeat_source.species_source.species_from_list == 'yes'
model_org=${repeat_masking.repeat_source.species_source.species_list}
@@ -123,6 +132,11 @@
rmlib= # provide an organism specific repeat library in fasta format for RepeatMasker
softmask=${repeat_masking.repeat_source.softmask} # use soft-masking rather than hard-masking in BLAST (i.e. seg and dust filtering)
+#else if $repeat_masking.repeat_source.source_type == 'dfam_up'
+model_org=${repeat_masking.repeat_source.species_name}
+rmlib= # provide an organism specific repeat library in fasta format for RepeatMasker
+softmask=${repeat_masking.repeat_source.softmask} # use soft-masking rather than hard-masking in BLAST (i.e. seg and dust filtering)
+
#else if $repeat_masking.repeat_source.source_type == 'library'
model_org= # select a model organism for RepBase masking in RepeatMasker
#if $repeat_masking.repeat_source.rmlib
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