Menu ▾ ▴

#12 Installation script to configure paths to blast and scratch

1.0
open
Jason Miller
None
2016-05-24
2016-05-24
Jason Miller
No

The installation config or make process should establish paths to resources on the host filesystem. Right now, there are hard-coded paths in a csh script. Hosts may have perl somewhere other than /usr/local/bin and they may not even have /usr/local/scratch. (Not to mention non-unix hosts.)

prod3/createSymLinks.csh
ln -s /usr/local/bin/blastall ./blastall
ln -s /usr/local/bin/cd-hit ./cd-hit
ln -s /usr/local/bin/clustalw2 ./clustalw
ln -s /usr/local/bin/fastacmd ./fastacmd
ln -s /usr/local/bin/formatdb ./formatdb
ln -s /usr/local/bin/muscle ./muscle
ln -s /usr/local/bin/perl ./perl
ln -s /usr/local/scratch/VIRAL/VIGOR/tempspace ./vigorscratch

Note that this script has no error checking; when it fails silenty, the user gets errors downstream and the error messages are confusing. Here is an example.

Problems executing the following command: "/Users/jmiller/Source/Vigor/jcvi-vigor-code/trunk/prod3/fastacmd -d /Users/jmiller/Source/Vigor/jcvi-vigor-code/trunk/data3/yfv_db -I 2> /dev/null" (Error Number: "32512" - Child error message: "")

Discussion

  • Jason Miller

    Jason Miller - 2016-05-24
    • assigned_to: Jason Miller
     

  • Jason Miller

    Jason Miller - 2016-05-24
    • Description has changed:

    Diff:

    --- old
+++ new
@@ -1,4 +1,4 @@
-The installation config or make process should establish paths to resources on the host filesystem. Right now, there are hard-coded paths in a csh script. Hosts may have perl somewhere other than /usr/local/bin and they may not even have /usr/local/scratch. (Not to mention non-unix hosts.)
+The installation config or make process should establish paths to resources on the host filesystem. Right now, there are hard-coded paths in a csh script. Hosts may have perl somewhere other than /usr/local/bin and they may not even have /usr/local/scratch. (Not to mention non-unix hosts.) 

 prod3/createSymLinks.csh 
 ln -s /usr/local/bin/blastall ./blastall
@@ -9,3 +9,9 @@
 ln -s /usr/local/bin/muscle ./muscle
 ln -s /usr/local/bin/perl ./perl
 ln -s /usr/local/scratch/VIRAL/VIGOR/tempspace ./vigorscratch
+
+Note that this script has no error checking; when it fails silenty, the user gets errors downstream and the error messages are confusing. Here is an example.
+
+Problems executing the following command: "/Users/jmiller/Source/Vigor/jcvi-vigor-code/trunk/prod3/fastacmd -d /Users/jmiller/Source/Vigor/jcvi-vigor-code/trunk/data3/yfv_db -I 2> /dev/null" (Error Number: "32512" - Child error message: "")
+
+
     

Log in to post a comment.