Mercurial > repos > iuc > hyphy_bgm

changeset 2:f2c6ada85b41 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f14f2bae2b27dc04e574803c7d4442a64cfe43e4"
author iuc
date Fri, 14 Feb 2020 16:43:36 -0500
parents cdfa1afd7cb0
children 1df765cc6bcb
files hyphy_bgm.xml macros.xml
diffstat 2 files changed, 3 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- a/hyphy_bgm.xml	Thu Feb 13 15:00:37 2020 -0500
+++ b/hyphy_bgm.xml	Fri Feb 14 16:43:36 2020 -0500
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="hyphy_bgm" name="HyPhy-BGM" version="@VERSION@+galaxy0">
+<tool id="hyphy_bgm" name="HyPhy-BGM" version="@VERSION@+galaxy1">
     <description>- Detecting coevolving sites via Bayesian graphical models</description>
     <macros>
         <import>macros.xml</import>
@@ -8,7 +8,7 @@
     <command detect_errors="exit_code"><![CDATA[
         ln -s '$input_file' bgm_input.fa &&
         ln -s '$input_nhx' bgm_input.nhx &&
-        @HYPHY_INVOCATION@ bgm
+        hyphy bgm
             --alignment ./bgm_input.fa
             --tree ./bgm_input.nhx
             --run_type $datatype.value
--- a/macros.xml	Thu Feb 13 15:00:37 2020 -0500
+++ b/macros.xml	Fri Feb 14 16:43:36 2020 -0500
@@ -80,6 +80,7 @@
             <yield/>
         </requirements>
     </xml>
+    <token name="@HYPHYMPI@">mpirun -np \${GALAXY_SLOTS:-1} HYPHYMPI</token>
     <token name="@HYPHY_ENVIRONMENT@"><![CDATA[export HYPHY=`which hyphy` &&
 export HYPHY_PATH=`dirname \$HYPHY` &&
 export HYPHY_LIB=`readlink -f \$HYPHY_PATH/../lib/hyphy` &&]]></token>