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: "")
Diff: