Hi, I generally tend to encourage others to first right a shell script which automates the build sequence. This often proves invaluable, in order to highlight the shortcomings -and often buggy- procedures of certain applications.
Eventually, the shell script tends to be trimmed down to the essential, as components of its functionality get replaced by EB processes. IMHO, this technique could apply here, too. (and just send the shell script here, if in doubt) F. On Sep 11, 2015, at 12:42 PM, Kenneth Hoste <[email protected]> wrote: > Hi Niek, > > Using a non-empty mail subject is recommended. ;-) > > On 11/09/15 12:26, Niek de Klein wrote: >> Hi all, >> >> I can't find an easyblock for this but maybe I have overlooked it so: >> I'm trying to install HOMER, which is installed by putting >> "configureHomer.pl" in the folder where you want to have HOMER installed (so >> this should not go to /sourcres/h/Homer but to the installation folder), and >> then have to run >> >> perl configureHomer.pl >> >> I haven't found an EasyBlock that uses perl to install programs though, is >> one already available? Here is the EB I have so far: >> >> >> easyblock = 'EB_HOMER' # tried to make my own easyblock that uses perl >> but did not work >> name = 'HOMER' >> version = 'master' >> >> homepage = 'http://homer.salk.edu/homer/' >> description = """HOMER (Hypergeometric Optimization of Motif EnRichment) is >> a suite of tools for Motif Discovery.""" >> >> toolchain = {'name': 'goolf', 'version': '1.7.20'} >> >> source_urls = ['http://homer.salk.edu/homer/'] >> sources = ['configureHomer.pl'] > > No versioning? :( > >> >> >> executables = >> ['makeTagDirectory','findPeaks','mergePeaks','genomeOntology','getPeakTags','makeUCSCfile', >> 'getDifferentialPeaks', 'assignGenomeAnnotation', >> 'homerTools','homer','homer2','analyzeHiC', >> 'getGenomeTilingPeaks'] >> >> files_to_copy = [(executables,'bin')] >> >> dependencies = [ >> ('Ghostscript', '9.16'), >> ('Weblogo', '2.8.2', '', True), >> ('BLAT', '3.5'), >> ] >> >> moduleclass = 'bio' > > Maybe take a look at the CmpCp easyblock. It derives from MakeCp, and > provides support for something like this (untested): > > cmds_map = [('configureHomer.pl', 'perl configureHomer.pl')] > > > If you want help with the EB_HOMER easyblock, let's see it. :-) > > > regards, > > Kenneth -- echo "sysadmin know better bash than english" | sed s/min/mins/ \ | sed 's/better bash/bash better/' # signal detected in a CERN forum
