Remove CONDA_PREFIX references.

reid-wagner · Jul 9, 2024 · 68fb04a · 68fb04a
1 parent 5732dfa
commit 68fb04a
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Showing 2 changed files with 4 additions and 3 deletions.
diff --git a/tools/fragpipe/fragpipe.xml b/tools/fragpipe/fragpipe.xml
@@ -41,10 +41,10 @@
                 --ram \$[ \${GALAXY_MEMORY_MB:-8192} / 1024 ]
                 --workflow fp.workflow --manifest fp.manifest
                 --workdir outputs
-                --config-msfragger \${CONDA_PREFIX}/share/msfragger-*/MSFragger-*/MSFragger-*.jar
+                --config-msfragger \${env_location}/share/msfragger-*/MSFragger-*/MSFragger-*.jar
                 --config-philosopher \$(which philosopher)
                 --config-python \$(which python)
-                --config-ionquant \${CONDA_PREFIX}/share/ionquant-*/IonQuant.jar &&
+                --config-ionquant \${env_location}/share/ionquant-*/IonQuant.jar &&
 
             @PREPARE_OUTPUTS@
         #end if

diff --git a/tools/fragpipe/macros.xml b/tools/fragpipe/macros.xml
@@ -31,7 +31,8 @@
       Prepares enviroment variables for FragPipe.
     -->
     <token name="@PREPARE_ENVIRONMENT@"><![CDATA[
-        cp -r \${CONDA_PREFIX}/share/fragpipe*/ fragpipe_local/ &&
+        env_location="\$(dirname \$(which philosopher))/.." &&
+        cp -r \${env_location}/share/fragpipe*/ fragpipe_local/ &&
         mkdir .cache .config tmp &&
         export XDG_CONFIG_HOME=\$(pwd)/.config &&
         export XDG_CACHE_HOME=\$(pwd)/.cache &&