{bio}[foss/2020b] ABRA2 v2.23, CRISPR-DAV v2.3.4, Excel-Writer-XLSX v1.09, FLASH v2.2.00, PRINSEQ v0.20.4, pysamstats v1.1.2 w/ Python 3.8.6 #13139

deniskristak · 2021-06-14T11:18:21Z

(created using eb --new-pr)

requires ~~easybuilders/easybuild-easyblocks#2487~~ (CRISPR-DAV easyblock) + ~~#13762~~ (naturalsort extension for R)

…-foss-2020b.eb, Excel-Writer-XLSX-1.09-foss-2020b.eb

easybuild/easyconfigs/e/Excel-Writer-XLSX/Excel-Writer-XLSX-1.09-foss-2020b.eb

easybuild/easyconfigs/n/naturalsort/naturalsort-0.1.3-foss-2020b.eb

easybuild/easyconfigs/p/pysamstats/pysamstats-1.1.2-foss-2020b.eb

deniskristak · 2021-06-15T13:13:13Z

please dont merge yet, ive added crispr-dav, but it still needs work

deniskristak · 2021-06-23T13:38:47Z

must be used with easybuilders/easybuild-easyblocks#2487

easybuild/easyconfigs/c/crispr-dav/crispr-dav-2.3.4-foss-2020b.eb

easybuild/easyconfigs/c/crispr-dav/crispr-dav-2.3.4-foss2020b_remove_hardcoding.patch

deniskristak · 2021-06-29T12:25:21Z

pushed to easyblock PR as well

deniskristak · 2021-07-01T09:14:59Z

ready for review, @boegel

deleting old file (has old filename)

adding archive-zip perl module

easybuild/easyconfigs/c/CRISPR-DAV/CRISPR-DAV-2.3.4-foss-2020b.eb

boegel · 2021-08-18T10:09:14Z

easybuild/easyconfigs/a/ABRA2/ABRA2-2.23-GCC-10.2.0.eb

+}
+
+modextravars = {
+    "LC_ALL": "en_US.UTF-8",


@deniskristak Hmm, why is this needed? That looks a bit fishy, it doesn't belong in a module generated by EasyBuild...

ABRA2 needs it because of this:
mozack/abra2#25

OK, please add a comment with a reference to that issue then:

# required to work around localization bug, see https://github.com/mozack/abra2/issues/25 modextravars = {'LC_ALL': 'en_US.UTF-8'}

easybuild/easyconfigs/c/CRISPR-DAV/CRISPR-DAV-2.3.4-foss-2020b.eb

easybuild/easyconfigs/f/FLASH/FLASH-2.2.00-foss-2020b.eb

easybuild/easyconfigs/n/naturalsort/naturalsort-0.1.3-foss-2020b.eb

easybuild/easyconfigs/p/pysamstats/pysamstats-1.1.2-foss-2020b.eb

easybuild/easyconfigs/e/Excel-Writer-XLSX/Excel-Writer-XLSX-1.09-foss-2020b.eb

removing old patch (moved to another folder)

…av-2.3.4_remove_hardcoding.patch renaming patchfile

renaming patchfile

better sanity check

better postinstallcmds

adding sanity_check_commands

removing, is an R extension

adding sanity_check_commands

removed naturalsort, added comment about it

deniskristak · 2021-08-19T09:53:31Z

@boegel ready for review

boegel · 2021-08-19T10:08:16Z

easybuild/easyconfigs/a/ABRA2/ABRA2-2.23-GCC-10.2.0.eb

+}
+
+modextravars = {
+    "LC_ALL": "en_US.UTF-8",


OK, please add a comment with a reference to that issue then:

# required to work around localization bug, see https://github.com/mozack/abra2/issues/25 modextravars = {'LC_ALL': 'en_US.UTF-8'}

easybuild/easyconfigs/a/ABRA2/ABRA2-2.23-GCC-10.2.0.eb

easybuild/easyconfigs/c/CRISPR-DAV/CRISPR-DAV-2.3.4-foss-2020b.eb

easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2020b-Perl-5.32.0.eb

boegel · 2021-08-19T15:30:52Z

Test report by @boegel
Using easyblocks from PR(s) easybuilders/easybuild-easyblocks#2487
SUCCESS
Build succeeded for 6 out of 6 (6 easyconfigs in total)
node3585.doduo.os - Linux RHEL 8.2, x86_64, AMD EPYC 7552 48-Core Processor (zen2), Python 3.6.8
See https://gist.github.com/511e361bb35aef80ba46503b62939e36 for a full test report.

boegel · 2021-08-19T15:31:50Z

Test report by @boegel
Using easyblocks from PR(s) easybuilders/easybuild-easyblocks#2487
SUCCESS
Build succeeded for 6 out of 6 (6 easyconfigs in total)
node3111.skitty.os - Linux centos linux 7.9.2009, x86_64, Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz, Python 3.6.8
See https://gist.github.com/90e614f57b3cca5a4eeb32b9439adba3 for a full test report.

boegel · 2021-08-19T15:31:51Z

@boegelbot please test @ generoso
EB_ARGS="--include-easyblocks-from-pr 2487"

boegelbot · 2021-08-19T15:35:09Z

@boegel: Request for testing this PR well received on generoso

PR test command 'EB_PR=13139 EB_ARGS="--include-easyblocks-from-pr 2487" /apps/slurm/default/bin/sbatch --job-name test_PR_13139 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 18161

Test results coming soon (I hope)...

- notification for comment with ID 902013446 processed

Message to humans: this is just bookkeeping information for me,
it is of no use to you (unless you think I have a bug, which I don't).

boegelbot · 2021-08-19T15:52:19Z

Test report by @boegelbot
Using easyblocks from PR(s) easybuilders/easybuild-easyblocks#2487
SUCCESS
Build succeeded for 6 out of 6 (6 easyconfigs in total)
generoso-c1-s-5 - Linux centos linux 8.2.2004, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/d2da4b0d02c37ed04bdea5e8099c0eed for a full test report.

boegel · 2021-08-19T17:19:56Z

Test report by @boegel
Using easyblocks from PR(s) easybuilders/easybuild-easyblocks#2487
SUCCESS
Build succeeded for 7 out of 7 (6 easyconfigs in total)
node3111.skitty.os - Linux centos linux 7.9.2009, x86_64, Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz, Python 3.6.8
See https://gist.github.com/7adad6dba709de77ae3ddb954ef48a24 for a full test report.

boegel

lgtm

boegel · 2021-08-20T07:41:57Z

Going in, thanks @deniskristak!

deniskristak added 4 commits June 14, 2021 13:18

adding easyconfigs: naturalsort-0.1.3-foss-2020b.eb, pysamstats-1.1.2…

c49ebef

…-foss-2020b.eb, Excel-Writer-XLSX-1.09-foss-2020b.eb

less strict requirements of pysamstats

af9d999

repaired source file name

c39a53a

changed http to https

a91aa34

boegel requested changes Jun 14, 2021

View reviewed changes

changes according to review

a9662fa

WIP removing hardcoded paths

69c6bdb

easybuilders deleted a comment from boegelbot Jun 15, 2021

functional crispr-dav

5443b56

flash2 should be accessible via flash cmd

974e09c

easybuilders deleted a comment from boegelbot Jun 28, 2021

boegel mentioned this pull request Jun 28, 2021

add custom easyblock for CRISPR-DAV easybuilders/easybuild-easyblocks#2487

Merged

boegel requested changes Jun 28, 2021

View reviewed changes

deniskristak mentioned this pull request Jun 29, 2021

{bio}[foss/2020b] CRISPResso2 v2.1.2 w/ Python 2.7.18 #13270

Merged

review changes

c06d427

deniskristak and others added 4 commits August 17, 2021 13:22

setting crisprdav easyblock explicitely

b8bf8f4

Delete crispr-dav-2.3.4-foss-2020b.eb

d2c98b1

deleting old file (has old filename)

removing explicit crispr-dav easyblock

0333231

Update CRISPR-DAV-2.3.4-foss-2020b.eb

fd5fbdc

adding archive-zip perl module

easybuilders deleted a comment from boegelbot Aug 18, 2021

boegel requested changes Aug 18, 2021

View reviewed changes

deniskristak added 5 commits August 18, 2021 19:13

Delete crispr-dav-2.3.4-foss2020b_remove_hardcoding.patch

7e59428

removing old patch (moved to another folder)

Rename crispr-dav-2.3.4-foss2020b_remove_hardcoding.patch to crispr-d…

59b8101

…av-2.3.4_remove_hardcoding.patch renaming patchfile

Update CRISPR-DAV-2.3.4-foss-2020b.eb

37abf2d

renaming patchfile

Create CRISPR-DAV-2.3.4-foss-2020b.eb

3b79f49

renaming patchfile

Update Excel-Writer-XLSX-1.09-foss-2020b.eb

daf8db7

better sanity check

deniskristak added 5 commits August 18, 2021 19:18

Update FLASH-2.2.00-foss-2020b.eb

852ce7a

better postinstallcmds

Update FLASH-2.2.00-foss-2020b.eb

37cc749

adding sanity_check_commands

Delete naturalsort-0.1.3-foss-2020b.eb

0464e66

removing, is an R extension

Update pysamstats-1.1.2-foss-2020b.eb

1b1c3c6

adding sanity_check_commands

Update CRISPR-DAV-2.3.4-foss-2020b.eb

f231d83

removed naturalsort, added comment about it

boegel changed the title ~~{tools}[foss/2020b] naturalsort v0.1.3, pysamstats v1.1.2, Excel-Writer-XLSX v1.09 w/ Python 3.8.6~~ {tools}[foss/2020b] ABRA2 v2.23, CRISPR-DAV v2.3.4, Excel-Writer-XLSX v1.09, FLASH v2.2.00, PRINSEQ v0.20.4, pysamstats v1.1.2 w/ Python 3.8.6 Aug 19, 2021

boegel requested changes Aug 19, 2021

View reviewed changes

boegel added new update labels Aug 19, 2021

boegel added this to the next release (4.4.2?) milestone Aug 19, 2021

fix suggestions for ABRA2, CRISPR-DAV, PRINSEQ easyconfigs

47df656

boegel force-pushed the 20210614131815_new_pr_naturalsort013 branch from bd32a16 to 47df656 Compare August 19, 2021 15:00

fix long line in Excel-Writer-XLSX easyconfig

db6b328

easybuilders deleted a comment from boegelbot Aug 19, 2021

boegel previously approved these changes Aug 19, 2021

View reviewed changes

stick to SAMtools 1.11 as dependency for CRISPR-DAV

c062a0e

boegel dismissed their stale review via c062a0e August 19, 2021 17:04

easybuilders deleted a comment from boegelbot Aug 19, 2021

boegel approved these changes Aug 20, 2021

View reviewed changes

boegel merged commit 0d57221 into easybuilders:develop Aug 20, 2021

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{bio}[foss/2020b] ABRA2 v2.23, CRISPR-DAV v2.3.4, Excel-Writer-XLSX v1.09, FLASH v2.2.00, PRINSEQ v0.20.4, pysamstats v1.1.2 w/ Python 3.8.6 #13139

{bio}[foss/2020b] ABRA2 v2.23, CRISPR-DAV v2.3.4, Excel-Writer-XLSX v1.09, FLASH v2.2.00, PRINSEQ v0.20.4, pysamstats v1.1.2 w/ Python 3.8.6 #13139

deniskristak commented Jun 14, 2021 •

edited by boegel

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{bio}[foss/2020b] ABRA2 v2.23, CRISPR-DAV v2.3.4, Excel-Writer-XLSX v1.09, FLASH v2.2.00, PRINSEQ v0.20.4, pysamstats v1.1.2 w/ Python 3.8.6 #13139

{bio}[foss/2020b] ABRA2 v2.23, CRISPR-DAV v2.3.4, Excel-Writer-XLSX v1.09, FLASH v2.2.00, PRINSEQ v0.20.4, pysamstats v1.1.2 w/ Python 3.8.6 #13139

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