[goolf/1.4.10, ictce/5.3.0] FSA, PRANK, SMALT, Infernal and deps (OK) by fgeorgatos · Pull Request #568 · easybuilders/easybuild-easyconfigs

fgeorgatos · 2013-11-29T13:46:00Z

i am cleaning up some bits from the easybuild.experimental repo, dragged on over previous months...

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

hpcugentbot · 2013-11-29T13:46:03Z

Automatic reply from Jenkins: Can I test this?

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

boegel · 2013-12-12T10:57:07Z

Jenkins: ok to test

boegel · 2013-12-22T21:39:27Z

please expand as in #624: 'simread', 'smalt', 'mixreads','readstats'

boegel · 2014-02-14T14:42:41Z

@fgeorgatos: several open remarks in this one...

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

fgeorgatos · 2014-02-15T02:47:41Z

all comments addressed, gn

boegel · 2014-04-17T15:44:51Z

in #802, @pescobar is suggesting to also add Exonorate as a dep (but its optional)?

AFAIK, optional - Exonerate is picked up if/when available

…onfigs into contrib_mroe_bioinfo

fgeorgatos · 2014-05-19T14:14:09Z

@pescobar: judicium on this one? this should provide for #802 needs as well

boegel · 2014-06-09T19:01:34Z

Test report by @boegel
FAILED
Build succeeded for 5 out of 13
Linux SL 6.5, Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz, Python 2.6.6
See https://gist.github.com/8ee3f8d615ab2d7b0a05 for a full test report.

boegel · 2014-06-09T19:54:17Z

missing dependency for Exonerate: fsm.h:24:37: fatal error: glib.h: No such file or directory
the Infernal build only failed because I need to seed the source file (download over ftp doesn't work on these systems)

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

fgeorgatos · 2014-06-10T00:58:52Z

OK, fixed it as per comments, please retry?

fgeorgatos · 2014-11-25T15:15:19Z

Test report by @fgeorgatos
FAILED
Build succeeded for 10 out of 16
Linux debian 6.0.10, Intel(R) Xeon(R) CPU L5640 @ 2.27GHz, Python 2.6.6
See https://gist.github.com/c821e2f4d45ba733b0a2 for a full test report.

fgeorgatos · 2014-12-17T00:16:40Z

@boegel: willing to test? this should be mergeable and avoid-dublicate-PRs-able ;-)

hpcugentbot · 2014-12-17T00:20:28Z

Test FAILed.

…onfigs into contrib_mroe_bioinfo

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

hpcugentbot · 2014-12-17T02:44:53Z

Test PASSed.

fgeorgatos · 2015-02-11T14:11:33Z

@boegel: status here?

We had closed a PR of @pescobar at some point and then this remained stale...

boegel · 2015-02-12T11:01:34Z

Jenkins: test this please

hpcugentbot · 2015-02-12T11:08:15Z

Refer to this link for build results (access rights to CI server needed):
https://jenkins1.ugent.be/job/easybuild-easyconfigs-pr-builder/2332/
Test FAILed.

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

hpcugentbot · 2015-02-12T11:29:02Z

Refer to this link for build results (access rights to CI server needed):
https://jenkins1.ugent.be/job/easybuild-easyconfigs-pr-builder/2335/
Test FAILed.

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

hpcugentbot · 2015-02-12T11:39:46Z

Refer to this link for build results (access rights to CI server needed):
https://jenkins1.ugent.be/job/easybuild-easyconfigs-pr-builder/2337/
Test PASSed.

boegel · 2015-02-12T12:06:00Z

Test report by @boegel
SUCCESS
Build succeeded for 15 out of 15 (15 easyconfigs in this PR)
Linux SL 6.6, Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz, Python 2.6.6
See https://gist.github.com/d30cca96d68cde45e7d1 for a full test report.

boegel · 2015-02-12T12:06:55Z

looking great, going in, thanks @fgeorgatos!

[goolf/1.4.10, ictce/5.3.0] FSA, PRANK, SMALT, Infernal and deps (WIP)

fgeorgatos · 2015-02-12T19:48:26Z

hallelujaj! ;-)

fgeorgatos · 2015-02-12T19:49:00Z

@boegel: and this is a good example of a PR that we could have exploited a long time ago ;-)

add FSA, PRANK & SMALT, coming from LCSB experimenters

1e05a6a

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

init Infernal 1.1

909b8db

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

fgeorgatos mentioned this pull request Dec 20, 2013

smalt-0.7.5-goolf-1.4.10.eb #624

Closed

boegel reviewed Dec 22, 2013
View reviewed changes

fgeorgatos added 5 commits February 15, 2014 03:17

fix Infernal source_urls with templating

f434037

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

adjust PRANK

5232769

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

add MAFFT for PRANK, make sure it's used

772c4dc

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

adjust SMALT builds

6488585

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

fix bug in SMALT

2bf00c6

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

boegel modified the milestones: v1.11, v1.10 Feb 15, 2014

boegel modified the milestones: v1.12, v1.11 Mar 14, 2014

fgeorgatos mentioned this pull request Apr 4, 2014

FSA-1.15.8-goolf-1.4.10.eb and Exonerate-2.2.0-goolf-1.4.10.eb #802

Closed

boegel reviewed Apr 17, 2014
View reviewed changes

Merge branch 'develop' of https://github.com/hpcugent/easybuild-easyc…

1799c9b

…onfigs into contrib_mroe_bioinfo

amend Exonerate easyconfigs with GLib dep

5cfe6a7

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

fgeorgatos mentioned this pull request Nov 8, 2014

Three new Bioinformatics packages, just version bumps #1186

Closed

fgeorgatos added 3 commits December 17, 2014 03:25

Merge branch 'develop' of https://github.com/hpcugent/easybuild-easyc…

a573020

…onfigs into contrib_mroe_bioinfo

add wherever: easyblock = 'ConfigureMake'

609a969

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

fix headers and trim whitespace

7003265

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

fgeorgatos changed the title ~~Contrib FSA, PRANK, SMALT, Infernal - and related~~ [goolf/1.4.10, ictce/5.3.0] FSA, PRANK, SMALT, Infernal and deps (WIP) Jan 20, 2015

bugfix filename of MAFFT for ictce/5.3.0

37e080a

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

really bugfix this MAFFT

16e6b57

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

boegel added a commit that referenced this pull request Feb 12, 2015

Merge pull request #568 from fgeorgatos/contrib_mroe_bioinfo

4041460

[goolf/1.4.10, ictce/5.3.0] FSA, PRANK, SMALT, Infernal and deps (WIP)

boegel merged commit 4041460 into easybuilders:develop Feb 12, 2015

boegel changed the title ~~[goolf/1.4.10, ictce/5.3.0] FSA, PRANK, SMALT, Infernal and deps (WIP)~~ [goolf/1.4.10, ictce/5.3.0] FSA, PRANK, SMALT, Infernal and deps (OK) Feb 12, 2015

fgeorgatos deleted the contrib_mroe_bioinfo branch February 12, 2015 19:48

Conversation

fgeorgatos commented Nov 29, 2013

Uh oh!

hpcugentbot commented Nov 29, 2013

Uh oh!

boegel commented Dec 12, 2013

Uh oh!

boegel Dec 22, 2013

Choose a reason for hiding this comment

Uh oh!

boegel commented Feb 14, 2014

Uh oh!

fgeorgatos commented Feb 15, 2014

Uh oh!

boegel Apr 17, 2014

Choose a reason for hiding this comment

Uh oh!

fgeorgatos Apr 29, 2014

Choose a reason for hiding this comment

Uh oh!

fgeorgatos commented May 19, 2014

Uh oh!

boegel commented Jun 9, 2014

Uh oh!

boegel commented Jun 9, 2014

Uh oh!

fgeorgatos commented Jun 10, 2014

Uh oh!

fgeorgatos commented Nov 25, 2014

Uh oh!

fgeorgatos commented Dec 17, 2014

Uh oh!

hpcugentbot commented Dec 17, 2014

Uh oh!

hpcugentbot commented Dec 17, 2014

Uh oh!

fgeorgatos commented Feb 11, 2015

Uh oh!

boegel commented Feb 12, 2015

Uh oh!

hpcugentbot commented Feb 12, 2015

Uh oh!

hpcugentbot commented Feb 12, 2015

Uh oh!

hpcugentbot commented Feb 12, 2015

Uh oh!

boegel commented Feb 12, 2015

Uh oh!

boegel commented Feb 12, 2015

Uh oh!

fgeorgatos commented Feb 12, 2015

Uh oh!

fgeorgatos commented Feb 12, 2015

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

3 participants