Mercurial > repos > iuc > maker

changeset 6:d46d803ca6cc draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 6ba137e32243a6de1fb83a7d4b88f9283db5dd01"
author iuc
date Tue, 05 Jan 2021 09:00:59 +0000
parents 5201ec38c01f
children 7bac6f5fcfa2
files maker.xml readme.rst
diffstat 2 files changed, 10 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/maker.xml	Mon Dec 28 23:19:04 2020 +0000
+++ b/maker.xml	Tue Jan 05 09:00:59 2021 +0000
@@ -39,9 +39,9 @@
             export AUGUSTUS_CONFIG_PATH=`pwd`/augustus_dir/ &&
         #end if
 
-        MPI_CMD="mpiexec -n \${GALAXY_SLOTS:-4}" &&
-        if [ "\$MAKER_NO_MPI" != "1" ]; then
-            MPI_CMD="";
+        MPI_CMD="" &&
+        if [ "\$MAKER_MPI" == "1" ]; then
+            MPI_CMD="mpiexec -n \${GALAXY_SLOTS:-4}";
         fi &&
 
         \${MPI_CMD} maker --ignore_nfs_tmp maker_opts.ctl maker_bopts.ctl maker_exe.ctl < /dev/null
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/readme.rst	Tue Jan 05 09:00:59 2021 +0000
@@ -0,0 +1,7 @@
+Running with MPI
+================
+
+By default, Maker will only run on 1 cpu. If you want to parallelize on any number
+of cpus and nodes, you can enable MPI by setting the ``MAKER_MPI`` variable to 1
+in the job destination, and setting ``GALAXY_SLOTS`` to the desired number of cores
+(see https://galaxyproject.org/admin/config/galaxy_slots/#galaxy_slots-for-server-admins).