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{bio}[foss/2020b] LncLOOM v2.0, MAFFT v7.475#12287

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boegel merged 2 commits intoeasybuilders:developfrom
zarybnicky:20210225190108_new_pr_LncLOOM20
Mar 5, 2021
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{bio}[foss/2020b] LncLOOM v2.0, MAFFT v7.475#12287
boegel merged 2 commits intoeasybuilders:developfrom
zarybnicky:20210225190108_new_pr_LncLOOM20

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@zarybnicky zarybnicky commented Feb 25, 2021

(created using eb --new-pr)

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zarybnicky commented Feb 25, 2021 •
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Includes a patch that forces the data specification files (for_eclip_annotation.txt and for_track_annotation.txt) to be specified via environment variables, given that the software requires multiple gigabytes of supporting data.

A workflow that I've tested:

pip -U install gdown
gdown https://drive.google.com/file/d/1ZyXCX1o7S4g0Ad_6wZU9esRNVzeqiNCc/view?usp=sharing
gdown https://drive.google.com/file/d/1PaU5kJvfC26fENF6E0H-fwLTimlW-e-8/view?usp=sharing

tar xvzf eCLIP_narrowPeakApr2019.tar.gz
tar xvzf hg19.tgz

cat > for_eclip_annotation.txt <<<EOS
Query Layer: 1
Blat: $(realpath hg19.fasta)
eCLIP: Data 1: $(realpath eCLIP_narrowPeakApr2019)
EOS

cat > for_track_annotation.txt <<<EOS
Query Layer: 1
Blat: $(realpath hg19.fasta)
EOS

export LNCLOOM_ECLIP_CONFIG=$(realpath for_eclip_annotation.txt)
export LNCLOOM_TRACK_CONFIG=$(realpath for_track_annotation.txt)
LncLOOM --targetscan --eclip --track --iterations 100 --multiprocess 6 --solver Gurobi --fasta <fasta>

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zarybnicky commented Feb 25, 2021

No idea what's the deal with JasPer though, it isn't anywhere in the dependency chain here.

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branfosj commented Feb 25, 2021

No idea what's the deal with JasPer though, it isn't anywhere in the dependency chain here.

The issues with JasPer will (hopefully) be fixed shortly (in #12288)

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@boegel boegel added this to the 4.x milestone Feb 26, 2021
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Comment thread easybuild/easyconfigs/l/LncLOOM/LncLOOM-2.0-foss-2020b.eb Outdated
@zarybnicky zarybnicky changed the title {bio}[foss/2020b] LncLOOM v2.0, MAFFT v7.475, Biopython v1.76 w/ Python 3.8.6 {bio}[foss/2020b] LncLOOM v2.0, MAFFT v7.475 Feb 26, 2021
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Comment thread easybuild/easyconfigs/l/LncLOOM/LncLOOM-2.0-environment.patch Outdated
Comment thread easybuild/easyconfigs/l/LncLOOM/LncLOOM-2.0-environment.patch Outdated
Comment thread easybuild/easyconfigs/l/LncLOOM/LncLOOM-2.0-foss-2020b.eb Outdated
@zarybnicky zarybnicky force-pushed the 20210225190108_new_pr_LncLOOM20 branch from da8a2a6 to 8ad0f30 Compare March 1, 2021 14:00
@zarybnicky
adding easyconfigs: LncLOOM-2.0-foss-2020b-Python-3.8.6.eb, MAFFT-7.4…
d5f51ea 
…75-gompi-2020b-with-extensions.eb, Biopython-1.76-foss-2020b-Python-3.8.6.eb and patches: LncLOOM-2.0-environment.patch

Squash:
LncLOOM: sanity_check -> postinstall
LncLOOM: Biopython-1.76-foss-2020b-Python-3.8.6.eb
LncLOOM: don't include python suffix
LncLOOM: delete LncLOOM-2.0-foss-2020b-Python-3.8.6.eb
LncLOOM: use Biopython 1.78, figure out pulptest
LncLOOM: Biopython-1.76-foss-2020b.eb
LncLOOM: extract gorubipy dependency
@zarybnicky zarybnicky force-pushed the 20210225190108_new_pr_LncLOOM20 branch from 8ad0f30 to d5f51ea Compare March 1, 2021 14:06
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Comment thread easybuild/easyconfigs/l/LncLOOM/LncLOOM-2.0-foss-2020b.eb Outdated
Comment thread easybuild/easyconfigs/l/LncLOOM/LncLOOM-2.0-foss-2020b.eb Outdated
Comment thread easybuild/easyconfigs/g/Gurobi/Gurobi-9.1.1-GCCcore-10.2.0.eb
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boegel commented Mar 2, 2021

Test report by @boegel
SUCCESS
Build succeeded for 4 out of 4 (4 easyconfigs in total)
node3517.doduo.os - Linux RHEL 8.2, x86_64, AMD EPYC 7552 48-Core Processor (zen2), Python 3.6.8
See https://gist.github.com/b81fb965d14e03d8bf5c50df9fb9b5e8 for a full test report.

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boegel commented Mar 2, 2021

Test report by @boegel
SUCCESS
Build succeeded for 4 out of 4 (4 easyconfigs in total)
node3100.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/1d38ec45a0782fc89defa90a6998a485 for a full test report.

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boegel commented Mar 2, 2021

Test report by @boegel
SUCCESS
Build succeeded for 4 out of 4 (4 easyconfigs in total)
node2602.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/142831bfdae2e031f0ff140d9350178b for a full test report.

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boegel commented Mar 5, 2021

@boegelbot please test @ generoso

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boegelbot commented Mar 5, 2021

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

PR test command 'EB_PR=12287 EB_ARGS= /apps/slurm/default/bin/sbatch --job-name test_PR_12287 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

  • exit code: 0
  • output:
Submitted batch job 16261

Test results coming soon (I hope)...

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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).

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boegelbot commented Mar 5, 2021

Test report by @boegelbot
FAILED
Build succeeded for 2 out of 4 (4 easyconfigs in total)
generoso-c1-s-1 - 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/78278ee3359748f70200432812b26afb for a full test report.

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zarybnicky commented Mar 5, 2021

Gurobi fails due to missing licence, is that fixable?

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boegel commented Mar 5, 2021

Gurobi fails due to missing licence, is that fixable?

Not on the generoso test system, but the test reports from the different HPC-UGent systems show it works, so not a blocker.

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boegel commented Mar 5, 2021

Going in, thanks @zarybnicky!

@boegel boegel merged commit 94f55e7 into easybuilders:develop Mar 5, 2021
@boegel boegel removed this from the 4.x milestone Mar 5, 2021
@boegel boegel added this to the next release (4.3.4?) milestone Mar 5, 2021
@zarybnicky zarybnicky deleted the 20210225190108_new_pr_LncLOOM20 branch March 5, 2021 12:26
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