Psortb foss2016a #3317

RvDijk · 2016-07-10T14:54:54Z

No description provided.

RvDijk · 2016-07-10T14:55:01Z

@boegel I'm not sure about how to name the dependency pftoolsV3

RvDijk · 2016-07-10T17:23:29Z

Dependency on ~~#3259~~

boegel · 2016-07-12T14:03:38Z

easybuild/easyconfigs/p/pftools/pftools-V3-foss-2016a.eb

+easyblock='ConfigureMake'
+
+name = 'pftools'
+version = 'V3'


@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?

boegel · 2016-07-13T15:46:29Z

easybuild/easyconfigs/p/pftools/pftoolsV3-24.03.16-foss-2016a.eb

+easyblock='ConfigureMake'
+
+name = 'pftoolsV3'
+version = '24.03.16'


@RvDijk I'd go with 20160324, i.e. the format we usually go for which sorts properly

boegel · 2016-07-13T15:46:55Z

(close/open to trigger Travis)

boegel · 2016-07-13T17:17:04Z

Test report by @boegel
FAILED
Build succeeded for 2 out of 4 (3 easyconfigs in this PR)
node2064.delcatty.os - Linux SL 6.7, Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz, Python 2.6.6
See https://gist.github.com/cb0b98d3dd55e01096709853aaf15e2c for a full test report.

boegel · 2016-07-13T17:34:26Z

Test report by @boegel
FAILED
Build succeeded for 1 out of 3 (3 easyconfigs in this PR)
node2507.golett.os - Linux centos linux 7.2.1511, Intel(R) Xeon(R) CPU E5-2680 v3 @ 2.50GHz, Python 2.7.5
See https://gist.github.com/5310885ee3e8989275e54d922cc469e7 for a full test report.

boegel · 2016-07-13T18:06:52Z

Test report by @boegel
FAILED
Build succeeded for 1 out of 3 (3 easyconfigs in this PR)
node2064.delcatty.os - Linux SL 6.7, Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz, Python 2.6.6
See https://gist.github.com/cc96a04acc38a6bf24a0e14160cbdbaf for a full test report.

boegel · 2016-07-13T18:30:18Z

Test report by @boegel
FAILED
Build succeeded for 1 out of 3 (3 easyconfigs in this PR)
node2507.golett.os - Linux centos linux 7.2.1511, Intel(R) Xeon(R) CPU E5-2680 v3 @ 2.50GHz, Python 2.7.5
See https://gist.github.com/63d107b82cd83b50ddda475135358002 for a full test report.

RvDijk · 2016-07-19T10:37:27Z

@boegel the download link works for me, maybe connection issues?

boegel · 2016-08-10T17:08:03Z

@RvDijk sorry, FTP is blocked by our firewall which explains the download issues, trying again...

boegel · 2016-08-10T17:09:17Z

@RvDijk this will need to be fixed though, Travis is tripping over a mismatch between the name and location of the pftoolsV3 easyconfig:

AssertionError: Easyconfig file
/home/travis/build/hpcugent/easybuild-easyconfigs/easybuild/easyconfigs/p/pftools/pftoolsV3-20160324-foss-2016a.eb
not in expected subdirectory easybuild/easyconfigs/p/pftoolsV3

boegel · 2016-08-10T17:32:54Z

Test report by @boegel
FAILED
Build succeeded for 2 out of 3 (3 easyconfigs in this PR)
node2602.swalot.os - Linux centos linux 7.2.1511, Intel(R) Xeon(R) CPU E5-2660 v3 @ 2.60GHz, Python 2.7.5
See https://gist.github.com/0154007f04781cd4db4282338d3f3528 for a full test report.

boegel · 2016-08-10T17:45:00Z

Test report by @boegel
FAILED
Build succeeded for 2 out of 3 (3 easyconfigs in this PR)
node2006.delcatty.os - Linux SL 6.7, Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz, Python 2.6.6
See https://gist.github.com/74ab44e1a0888afdddf2bdd640cf378c for a full test report.

boegel · 2016-08-11T09:32:21Z

@RvDijk missing Perl module?

External Module XML::RPC, XML Based RPC client, is not installed on this computer.

RvDijk · 2016-08-26T11:55:30Z

@boegel the installation file stated that BLAST+ does not work for PSORTb. The missing perl module should not be an issue:
"The XML::RPC in PSortb needs it for making calls to remote PSortb servers, if you don't plan to do this, ignore this warning"
Perhaps changing the BLAST+ solved the problem?

boegel · 2016-08-26T14:07:01Z

Test report by @boegel
SUCCESS
Build succeeded for 3 out of 3 (3 easyconfigs in this PR)
node2539.golett.os - Linux centos linux 7.2.1511, Intel(R) Xeon(R) CPU E5-2680 v3 @ 2.50GHz, Python 2.7.5
See https://gist.github.com/17fedda86972f20295a455ad0db9f0f5 for a full test report.

boegel · 2016-08-26T14:16:24Z

Test report by @boegel
FAILED
Build succeeded for 2 out of 3 (3 easyconfigs in this PR)
node2130.delcatty.os - Linux SL 6.8, Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz, Python 2.6.6
See https://gist.github.com/2ed299af0f31ab46cf461ee09e6c6083 for a full test report.

boegel · 2016-08-26T14:21:05Z

@RvDijk seems like the installation procedure has cc hardcoded as compiler somewhere, causing the system GCC being picked up rather than the one from the toolchain...

cc -c   -D_REENTRANT -D_GNU_SOURCE -fPIC -O2 -march=native -fwrapv -fno-strict-aliasing -pipe -fstack-protector-strong -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_FORTIFY_SOURCE=2 -O2   -DVERSION=\"0.01\" -DXS_VERSION=\"0.01\" -fPIC "-I/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/Perl/5.22.1-foss-2016a/lib/perl5/5.22.1/x86_64-linux-thread-multi/CORE"   binding.c
cc1: error: unrecognized command line option "-fstack-protector-strong"

boegel · 2016-08-29T09:00:39Z

easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4_CC.patch

+ # They may have been overridden via Makefile.PL or on the command line.
+ AR = ar
+-CC = cc
+CC = gcc


@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

boegel · 2016-08-29T12:08:50Z

Test report by @boegel
FAILED
Build succeeded for 2 out of 3 (3 easyconfigs in this PR)
node2427.golett.os - Linux centos linux 7.2.1511, Intel(R) Xeon(R) CPU E5-2680 v3 @ 2.50GHz, Python 2.7.5
See https://gist.github.com/513e0a5763ec6ef43a8a1ac409496e2e for a full test report.

boegel · 2016-08-29T12:23:12Z

Test report by @boegel
FAILED
Build succeeded for 2 out of 3 (3 easyconfigs in this PR)
node2062.delcatty.os - Linux SL 6.8, Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz, Python 2.6.6
See https://gist.github.com/1ef9cc5adc9cd20ccfc073e5e3725eb5 for a full test report.

boegel · 2016-08-29T15:28:23Z

easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4_CC.patch

+#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


@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 hardcoding cc

do a runtime patch of Makefile via prebuildopt using a sed command to change the harcoded CC =cc to CC ?= cc

boegel · 2016-08-30T09:47:45Z

lgtm

boegel · 2016-08-30T10:08:49Z

Test report by @boegel
SUCCESS
Build succeeded for 3 out of 3 (3 easyconfigs in this PR)
node2646.swalot.os - Linux centos linux 7.2.1511, Intel(R) Xeon(R) CPU E5-2660 v3 @ 2.60GHz, Python 2.7.5
See https://gist.github.com/9853b2c958f5b781b353c45d918653fa for a full test report.

boegel · 2016-08-30T10:43:33Z

Test report by @boegel
SUCCESS
Build succeeded for 3 out of 3 (3 easyconfigs in this PR)
node2050.delcatty.os - Linux SL 6.8, Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz, Python 2.6.6
See https://gist.github.com/6c5094e58e9e88502319ac4a7f9d01a6 for a full test report.

boegel · 2016-08-30T10:49:49Z

Going in, thanks @RvDijk!

RvDijk added 2 commits July 10, 2016 16:46

psortb with foss2016a

a9d2a80

BLAST+ in BLAST+ folder

f43ff29

RvDijk mentioned this pull request Jul 10, 2016

Text-CSV with foss2016a #3323

Merged

RvDijk added 2 commits July 10, 2016 18:28

include patch

a0b242a

include patch

6d1ac74

boegel reviewed Jul 12, 2016
View reviewed changes

boegel added this to the v2.9.0 milestone Jul 12, 2016

pftools rename, perlversion used properly

2746609

boegel reviewed Jul 13, 2016
View reviewed changes

boegel closed this Jul 13, 2016

boegel reopened this Jul 13, 2016

RvDijk added 3 commits July 13, 2016 18:32

version change, removed perlmajver

055e276

version change for pftoolsV3 dep

c3e97c9

format of date

75aa60a

RvDijk added 2 commits August 26, 2016 13:06

use BLAST instead of BLAST+

75f0cd7

use BLAST instead of BLAST+

a4ce580

RvDijk added 2 commits August 27, 2016 22:33

provide patch for hardcoded CC

dc39cdf

update patch file

113096c

boegel reviewed Aug 29, 2016
View reviewed changes

Update patch to inherit value from env

26042f4

boegel reviewed Aug 29, 2016
View reviewed changes

RvDijk added 2 commits August 30, 2016 11:25

use sed to remove hardcoded CC in makefile

2cb8101

Use sed for hardcoded CC and removed patch

64c793b

boegel merged commit 5c5ca4c into easybuilders:develop Aug 30, 2016

RvDijk deleted the psortb-foss2016a branch August 30, 2016 11:59

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Psortb foss2016a #3317

Psortb foss2016a #3317

RvDijk commented Jul 10, 2016

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Psortb foss2016a #3317

Psortb foss2016a #3317

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