After messing around a bit with EasyBuild I found that for the packages
I wanted it kept installing foss versions (not all were built with the
same foss), and each of these were entire compiler/bintools/etc. sets of
files. Seemed kind of ridiculous since I already knew how to build
those packages on Centos7, although sometimes devtoolset-7 was needed.
So a default environment of:
/usr/common/modules/el7/x86_64/modules/all/CentOS/vanilla.lua
was defined. This module does basically nothing, but provides a
reference in case some other variant CentOS based environment is ever
needed.
A script "module_generate_from_directory.sh" was written to
semi-automatically generate lua files from the install directories. I
should probably have written it in lua but it is bash for now. It makes
some conservative assumptions about
directory names, but even those may not always be valid, so the lua file
might need manual modification. Anyway, it is a start, and it gets it
right most of the time for packages which use "configure".
These two files are here:
http://saf.bio.caltech.edu/pub/software/linux_or_unix_tools/module_generate_from_directory.sh
http://saf.bio.caltech.edu/pub/software/linux_or_unix_tools/vanilla.lua
Here is an example of one of the few mod files which has needed manual
editing after it was generated:
module_generate_from_directory.sh \
augustus \
3.3.2\
CentOS/vanilla \
/usr/common/modules/el7/x86_64/software/augustus/3.3.2-CentOS-vanilla
\
"AUGUSTUS is a program that predicts genes in eukaryotic genomic
sequences." \
"http://bioinf.uni-greifswald.de/augustus/";
vi
/usr/common/modules/el7/x86_64/modules/all/augustus/3.3.2-CentOS-vanilla.lua
#-- added manually
#prepend_path("PATH", pathJoin(root, "scripts"))
#setenv("AUGUSTUS_CONFIG_PATH",pathJoin(root,"config"))
#scripts subdir is not automatically added because in some cases it
should NOT
#be on PATH.
module load augustus
module list
Currently Loaded Modules:
1) CentOS/vanilla 2) augustus/3.3.2-CentOS-vanilla
augustus 2>&1 | head -2
AUGUSTUS (3.3.2) is a gene prediction tool
written by M. Stanke, O. Keller, S. König, L. Gerischer and L. Romoth.
Regards,
David Mathog
mat...@caltech.edu
Manager, Sequence Analysis Facility, Biology Division, Caltech
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