{bio}[foss/2020b] RepeatModeler v2.0.2a

[jfgrimm]

(created using eb --new-pr)

Depends on easyconfigs:

• {bio}[GCC/10.2.0] GenomeTools v1.6.1 #13104
• {bio}[GCC/10.2.0] RECON v1.08 #13123
• {bio}[GCC/10.2.0] RepeatScout v1.0.6 #13124
• {bio}[GCC/10.2.0,foss/2020b] LTR_retriever v2.9.0, NINJA v0.97-cluster_only #13125

and the custom easyblock:

• new easyblock for RepeatModeler easybuild-easyblocks#2470

[verdurin]

@boegelbot please test @ generoso
EB_ARGS=" --include-easyblocks-from-pr=2470"

[boegelbot]

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

PR test command 'EB_PR=13126 EB_ARGS=" --include-easyblocks-from-pr=2470" /apps/slurm/default/bin/sbatch --job-name test_PR_13126 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

• exit code: 0
• output:

Submitted batch job 18137

Test results coming soon (I hope)...

- notification for comment with ID 898865749 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).

[verdurin]

On one of my test systems:

[compile canvas_cairo_file.o]
In file included from src/annotationsketch/canvas_cairo_context.c:30:
/mnt/ds918plus/eb/nuc-fedora32/build/GenomeTools/1.6.1/GCC-10.2.0/genometools-1.6.1/src/annotationsketch/canvas_cairo_context.h:21:10: fatal error: cairo.h: No such file or directory
   21 | #include <cairo.h>
      |          ^~~~~~~~~
compilation terminated.
In file included from src/annotationsketch/canvas_cairo.c:34:
/mnt/ds918plus/eb/nuc-fedora32/build/GenomeTools/1.6.1/GCC-10.2.0/genometools-1.6.1/src/annotationsketch/graphics_cairo_api.h:21:10: fatal error: cairo.h: No such file or directory
   21 | #include <cairo.h>
      |          ^~~~~~~~~
compilation terminated.
make: *** [Makefile:824: obj/src/annotationsketch/canvas_cairo.o] Error 1
make: *** Waiting for unfinished jobs....
make: *** [Makefile:824: obj/src/annotationsketch/canvas_cairo_context.o] Error 1
In file included from src/annotationsketch/canvas_cairo_file.c:34:
/mnt/ds918plus/eb/nuc-fedora32/build/GenomeTools/1.6.1/GCC-10.2.0/genometools-1.6.1/src/annotationsketch/graphics_cairo_api.h:21:10: fatal error: cairo.h: No such file or directory
   21 | #include <cairo.h>
      |          ^~~~~~~~~
compilation terminated.
make: *** [Makefile:824: obj/src/annotationsketch/canvas_cairo_file.o] Error 1

[boegelbot]

Test report by @boegelbot
Using easyblocks from PR(s) easybuilders/easybuild-easyblocks#2470
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
generoso-x-2 - 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/e859d386f89631a1c306e4c025f502dc for a full test report.

[jfgrimm]

@verdurin can you try adding pkg-config as a builddep to GenomeTools, to see if that fixes the issue?

[verdurin]

Test report by @verdurin
Using easyblocks from PR(s) easybuilders/easybuild-easyblocks#2470
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
nuc.lan - Linux Fedora 33, x86_64, Intel(R) Core(TM) i7-8650U CPU @ 1.90GHz, Python 3.9.6
See https://gist.github.com/7ba78d006044ab7fba2a2cc987a47c59 for a full test report.

[verdurin]

@jfgrimm looks like a rebuilt GenomeTools with that change did indeed fix the issue for me - thanks.

[boegel]

Test report by @boegel
Using easyblocks from PR(s) easybuilders/easybuild-easyblocks#2470
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
node3567.doduo.os - Linux RHEL 8.2, x86_64, AMD EPYC 7552 48-Core Processor (zen2), Python 3.6.8
See https://gist.github.com/5742d4b8fbf64da9208aed7dd3318964 for a full test report.

[boegel]

@boegelbot please test @ generoso
EB_ARGS=" --include-easyblocks-from-pr=2470"

[boegelbot]

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

PR test command 'EB_PR=13126 EB_ARGS=" --include-easyblocks-from-pr=2470" /apps/slurm/default/bin/sbatch --job-name test_PR_13126 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

• exit code: 0
• output:

Submitted batch job 18230

Test results coming soon (I hope)...

- notification for comment with ID 907375860 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]

Test report by @boegelbot
Using easyblocks from PR(s) easybuilders/easybuild-easyblocks#2470
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
generoso-c1-s-6 - 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/ad5f12cdd4a9f67923269ab15df4e48e for a full test report.

[boegel]

Test report by @boegel
Using easyblocks from PR(s) easybuilders/easybuild-easyblocks#2470
SUCCESS
Build succeeded for 21 out of 21 (1 easyconfigs in total)
node2723.swalot.os - Linux centos linux 7.9.2009, x86_64, Intel(R) Xeon(R) CPU E5-2660 v3 @ 2.60GHz (haswell), Python 3.6.8
See https://gist.github.com/ee9d8433fd7f49dfca41018ec9441061 for a full test report.

[boegel]

lgtm

[boegel]

Going in, thanks @jfgrimm!