{bio}[GCC/4.8.4] biocompressors: DSRC-2.0rc, fastqz-1.5, fqzcomp-4.6, Quip-1.1.8, SCALCE-2.7, ZPAQ-7.00 (REVIEW) by fgeorgatos · Pull Request #1242 · easybuilders/easybuild-easyconfigs

fgeorgatos · 2014-12-10T10:56:56Z

Signed-off-by: Fotis Georgatos [email protected]

Signed-off-by: Fotis Georgatos <[email protected]>

hpcugentbot · 2014-12-10T11:00:55Z

Test PASSed.

hpcugentbot · 2014-12-10T11:04:48Z

Test PASSed.

Signed-off-by: Fotis Georgatos <[email protected]>

hpcugentbot · 2014-12-10T11:15:01Z

Test PASSed.

hpcugentbot · 2014-12-10T12:06:31Z

Test PASSed.

hpcugentbot · 2014-12-10T18:01:32Z

Test FAILed.

hpcugentbot · 2014-12-10T18:12:12Z

Test PASSed.

fgeorgatos · 2015-01-20T13:03:14Z

Test report by @fgeorgatos
SUCCESS
Build succeeded for 6 out of 6
Linux debian 6.0.10, Intel(R) Xeon(R) CPU L5640 @ 2.27GHz, Python 2.6.6
See https://gist.github.com/3c2ce0d7182c479d13a0 for a full test report.

fgeorgatos · 2015-01-20T13:05:50Z

@boegel: DSRC is currently provided via github only, so the Binary version has been preferred for now; if this is an issue, I could drop it from this PR. Otherwise, we just need one more review over here.

boegel · 2015-01-20T13:19:19Z

versionless 'source', so include a checksum for it?

and I'd prefer %(namelower)s

boegel · 2015-01-20T13:24:26Z

Jenkins: test this please

hpcugentbot · 2015-02-06T07:02:13Z

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Test FAILed.

Signed-off-by: Fotis Georgatos <[email protected]>

hpcugentbot · 2015-02-06T07:09:39Z

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Test PASSed.

fgeorgatos · 2015-02-06T07:13:03Z

Test report by @fgeorgatos
SUCCESS
Build succeeded for 7 out of 7
Linux debian 6.0.10, Intel(R) Xeon(R) CPU X5670 @ 2.93GHz, Python 2.6.6
See https://gist.github.com/e64ec34a0a9515e5b306 for a full test report.

hpcugentbot · 2015-02-06T07:14:01Z

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fgeorgatos · 2015-02-06T07:14:03Z

OK, here it is; bug fixed and retested. Just make your judicium on the pod2man bit.

fgeorgatos · 2015-02-06T07:14:40Z

Test report by @fgeorgatos
SUCCESS
Build succeeded for 7 out of 7
Linux debian 6.0.10, Intel(R) Xeon(R) CPU E5-2660 0 @ 2.20GHz, Python 2.6.6
See https://gist.github.com/6d7299ff33e107c99409 for a full test report.

boegel · 2015-02-06T21:43:38Z

Either include a build dependency for pod2man, or remove this all together...

As is, this is a liability for breaking this build...

This is interesting:

$ rpm -q --whatprovides `which pod2man` perl-5.10.1-136.el6.x86_64

and indeed:

$ module load Perl/5.16.3-goolf-1.4.10-bare $ which pod2man /gpfs/scratch/projects/project_gpilot/vsc40023/software/Perl/5.16.3-goolf-1.4.10-bare/bin/pod2man

So, adding a Perl build on top of GCC/4.8.2 in here as a build dependency would do it!

see fgeorgatos#35

add Perl as build dep for ZPAQ

fgeorgatos · 2015-02-07T06:43:07Z

@boegel:
I have some doubts if we should add the most recent Perl as a builddep for a manpage;
however, that should not be a blocker for the whole PR, so now it's MERGED!

hpcugentbot · 2015-02-07T06:46:03Z

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Test FAILed.

boegel · 2015-02-07T09:03:12Z

@fgeorgatos: the only alternative is removed the use of pod2man... And it's not unlikely that these bioinfo people will like having Perl around anyway ;-)

…onfig

boegel · 2015-02-07T09:20:31Z

@fgeorgatos: this needs fgeorgatos#36...

include missing '-bare' versionsuffix for Perl builddep in ZPAQ easyconfig

fgeorgatos · 2015-02-07T09:24:50Z

@boegel: OK, merged; I think we (I) have entered bikesheding mode, so I just let go ;-)

boegel · 2015-02-07T10:04:03Z

Test report by @boegel
SUCCESS
Build succeeded for 8 out of 8 (8 easyconfigs in this PR)
Linux SL 6.5, Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz, Python 2.6.6
See https://gist.github.com/b1e06431599384e6a510 for a full test report.

hpcugentbot · 2015-02-07T10:07:29Z

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Test PASSed.

boegel · 2015-02-07T10:22:28Z

Looking great now, going in. Thanks @fgeorgatos!

{bio}[GCC/4.8.4] DSRC-2.0rc, fastqz-1.5, fqzcomp-4.6, Quip-1.1.8, SCALCE-2.7, ZPAQ-7.00 (REVIEW)

fgeorgatos · 2015-09-30T10:10:39Z

Pointers for future work under the same thread (if anybody gets interested in this anytime soon):

also, keep an eye on: http://ga4gh.org/#/fileformats-team

fgeorgatos added 2 commits December 10, 2014 11:56

add Quip

5cfb9de

Signed-off-by: Fotis Georgatos <[email protected]>

state which toolchain

6e0b86d

Signed-off-by: Fotis Georgatos <[email protected]>

fgeorgatos changed the title ~~add Quip~~ add biocompressors (Quip et al) Dec 10, 2014

supply working version of quip plz

c0950bb

Signed-off-by: Fotis Georgatos <[email protected]>

add ZPAQ

d4556c4

fgeorgatos added 5 commits December 10, 2014 17:58

add fqzcomp

98297d8

add DSRC

5b45bf8

add SCALCE

d607a2a

ZPAQ is really bio category

37b4af6

add fastqz

6830a0e

fix tiny little bugs, left & right

d40818d

fgeorgatos changed the title ~~add biocompressors (Quip et al)~~ add biocompressors (DSRC, fastqz, fqzcomp, Quip, SCALCE, ZPAQ et al) Dec 10, 2014

fgeorgatos changed the title ~~add biocompressors (DSRC, fastqz, fqzcomp, Quip, SCALCE, ZPAQ et al)~~ [GCC/4.8.2] add biocompressors (DSRC, fastqz, fqzcomp, Quip, SCALCE, ZPAQ et al) ; (REVIEW) Jan 20, 2015

boegel reviewed Jan 20, 2015
View reviewed changes

fgeorgatos added 2 commits February 6, 2015 08:05

bump to ZPAQ/7.00, really, also deps

94a14df

Signed-off-by: Fotis Georgatos <[email protected]>

ZPAQ/7.00 and commit the sanity test bugfix

02468aa

Signed-off-by: Fotis Georgatos <[email protected]>

fgeorgatos changed the title ~~{bio}[GCC/4.8.4] DSRC-2.0rc, fastqz-1.5, fqzcomp-4.6, Quip-1.1.8, SCALCE-2.7, ZPAQ-6.57 (REVIEW)~~ {bio}[GCC/4.8.4] DSRC-2.0rc, fastqz-1.5, fqzcomp-4.6, Quip-1.1.8, SCALCE-2.7, ZPAQ-7.00 (REVIEW) Feb 6, 2015

boegel reviewed Feb 6, 2015
View reviewed changes

add Perl as build dep for ZPAQ

0b0a5f0

boegel mentioned this pull request Feb 6, 2015

add Perl as build dep for ZPAQ fgeorgatos/easybuild-easyconfigs#35

Merged

Merge pull request #35 from boegel/contrib_biocompressors

2595b90

add Perl as build dep for ZPAQ

include missing '-bare' versionsuffix for Perl builddep in ZPAQ easyc…

5715d08

…onfig

boegel mentioned this pull request Feb 7, 2015

include missing '-bare' versionsuffix for Perl builddep in ZPAQ easyconfig fgeorgatos/easybuild-easyconfigs#36

Merged

Merge pull request #36 from boegel/contrib_biocompressors

a4e2d6e

include missing '-bare' versionsuffix for Perl builddep in ZPAQ easyconfig

boegel added a commit that referenced this pull request Feb 7, 2015

Merge pull request #1242 from fgeorgatos/contrib_biocompressors

aa8b118

{bio}[GCC/4.8.4] DSRC-2.0rc, fastqz-1.5, fqzcomp-4.6, Quip-1.1.8, SCALCE-2.7, ZPAQ-7.00 (REVIEW)

boegel merged commit aa8b118 into easybuilders:develop Feb 7, 2015

fgeorgatos deleted the contrib_biocompressors branch February 7, 2015 18:24

fgeorgatos changed the title ~~{bio}[GCC/4.8.4] DSRC-2.0rc, fastqz-1.5, fqzcomp-4.6, Quip-1.1.8, SCALCE-2.7, ZPAQ-7.00 (REVIEW)~~ {bio}[GCC/4.8.4] biocompressors: DSRC-2.0rc, fastqz-1.5, fqzcomp-4.6, Quip-1.1.8, SCALCE-2.7, ZPAQ-7.00 (REVIEW) May 29, 2015

fgeorgatos mentioned this pull request Jun 3, 2015

SCALCE-2.7 easyconfigs for goolf and ictce #865

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