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Psortb foss2016a #3317
Psortb foss2016a #3317
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@boegel I'm not sure about how to name the dependency pftoolsV3 |
Dependency on |
easyblock='ConfigureMake' | ||
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name = 'pftools' | ||
version = 'V3' |
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@RvDijk seems like pftoolsV3
is the software name?
and since the tarball isn't properly versioned, using a datestamp as version and add a checksum for the source tarball?
easyblock='ConfigureMake' | ||
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name = 'pftoolsV3' | ||
version = '24.03.16' |
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@RvDijk I'd go with 20160324
, i.e. the format we usually go for which sorts properly
(close/open to trigger Travis) |
Test report by @boegel |
Test report by @boegel |
Test report by @boegel |
Test report by @boegel |
@boegel the download link works for me, maybe connection issues? |
@RvDijk sorry, FTP is blocked by our firewall which explains the download issues, trying again... |
@RvDijk this will need to be fixed though, Travis is tripping over a mismatch between the name and location of the pftoolsV3 easyconfig:
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Test report by @boegel |
Test report by @boegel |
@RvDijk missing Perl module?
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@boegel the installation file stated that BLAST+ does not work for PSORTb. The missing perl module should not be an issue: |
Test report by @boegel |
Test report by @boegel |
@RvDijk seems like the installation procedure has
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# They may have been overridden via Makefile.PL or on the command line. | ||
AR = ar | ||
-CC = cc | ||
+CC = gcc |
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@RvDijk it's better/safer to use this construct, which should result in inheriting the $CC
value from the environment, and only use gcc
if it's not defined:
CC ?= gcc
Test report by @boegel |
Test report by @boegel |
#Subtitue hardcoded cc for gcc to prevent 'cc1: error: unrecognized command line option "-fstack-protector-strong"' | ||
#Author: Ruben van Dijk (University of Groningen) | ||
--- bio-tools-psort-all/bio-tools-psort-modhmm/Makefile 2016-08-29 09:40:30.000000000 +0200 | ||
+++ bio-tools-psort-all/bio-tools-psort-modhmm/Makefile 2016-08-29 09:40:14.000000000 +0200 |
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@RvDijk the patch doesn't work because the Makefile
file is generated at configure time...
Two options:
- patch
Makefile.PL
instead, which involves grabbing the value of$CC
in Perl from the environment rather than hardcodingcc
- do a runtime patch of
Makefile
viaprebuildopt
using ased
command to change the harcodedCC =cc
toCC ?= cc
lgtm |
Test report by @boegel |
Test report by @boegel |
Going in, thanks @RvDijk! |
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