Mercurial > repos > mingchen0919 > statonlab_interprocan

diff interproscan.Rmd @ 2:3e4a0719caa7 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
update
author mingchen0919
date Tue, 03 Apr 2018 15:06:55 -0400
parents 035457a30aea
children 10acf59ba351
line wrap: on
line diff
--- a/interproscan.Rmd	Tue Apr 03 15:02:39 2018 -0400
+++ b/interproscan.Rmd	Tue Apr 03 15:06:55 2018 -0400
@@ -14,6 +14,10 @@
 # InterProScan job script
 
 ```{bash echo=FALSE}
+# create two directorys: tempdir and output-dir
+mkdir -p ${X_d}/temp_dir
+mkdir -p ${X_d}/output_dir
+
 #---- build job script ----
 cat >temp.sh <<EOL
 /opt/main/InterProScan/5.28-67.0/interproscan.sh \\
@@ -23,8 +27,8 @@
   --iprlookup ${X_D} \\
   --goterms ${X_E} \\
   --pathways ${X_F} \\
-  --tempdir ${X_D}/temp_dir \\
-  --output-dir ${X_D}/output_dir > /dev/null 2>&1
+  --tempdir ${X_d}/temp_dir \\
+  --output-dir ${X_d}/output_dir > /dev/null 2>&1
   
 EOL