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

[zarybnicky]

(created using eb --new-pr)

[zarybnicky]

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>

[zarybnicky]

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

[branfosj]

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)

[boegel]

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.

[boegel]

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.

[boegel]

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.

[boegel]

@boegelbot please test @ generoso

[boegelbot]

@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)...

- notification for comment with ID 791262568 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
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.

[zarybnicky]

Gurobi fails due to missing licence, is that fixable?

[boegel]

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.

[boegel]

Going in, thanks @zarybnicky!