use patch to make ncbi-vdb 2.11.2 compatible with HDF5 1.12.2

[boegel]

ncbi-vdb 2.11.2 depending on HDF5 1.10.x makes it incompatible with other easyconfigs of the 2021b generation, R/4.1.2-foss-2021b for example, which causes problems (cfr. #17686)

There's an easy fix to make ncbi-vdb compatible with HDF5 1.12.x, which we already did for ncbi-vdb 3.0.0, see #17140

[boegel]

@boegelbot please test @ generoso
EB_ARGS="ncbi-vdb-2.11.2-gompi-2021b.eb HISAT2-2.2.1-gompi-2021b.eb SKESA-2.4.0-gompi-2021b_saute.1.3.0_1.eb shovill-1.1.0-gompi-2021b.eb"
CORE_CNT=16

[boegelbot]

@boegel: Request for testing this PR well received on login1

PR test command 'EB_PR=18236 EB_ARGS="ncbi-vdb-2.11.2-gompi-2021b.eb HISAT2-2.2.1-gompi-2021b.eb SKESA-2.4.0-gompi-2021b_saute.1.3.0_1.eb shovill-1.1.0-gompi-2021b.eb" EB_CONTAINER= /opt/software/slurm/bin/sbatch --job-name test_PR_18236 --ntasks="16" ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

• exit code: 0
• output:

Submitted batch job 11171

Test results coming soon (I hope)...

- notification for comment with ID 1613495796 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
SUCCESS
Build succeeded for 4 out of 4 (4 easyconfigs in total)
cnx1 - Linux Rocky Linux 8.5, x86_64, Intel(R) Xeon(R) CPU E5-2690 v3 @ 2.60GHz (haswell), Python 3.6.8
See https://gist.github.com/boegelbot/13acef69f31b5469760acc87bf248702 for a full test report.

[boegel]

Test report by @boegel
SUCCESS
Build succeeded for 4 out of 4 (4 easyconfigs in total)
node3169.skitty.os - Linux RHEL 8.6, x86_64, Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz (skylake_avx512), Python 3.6.8
See https://gist.github.com/boegel/46620bcfe829b9ea470635e694e79f4a for a full test report.

[Micket]

Test report by @Micket
SUCCESS
Build succeeded for 4 out of 4 (1 easyconfigs in total)
vera-c1 - Linux Rocky Linux 8.7, x86_64, Intel Xeon Processor (Skylake), Python 3.6.8
See https://gist.github.com/Micket/db882537a4d033e7934f4879d0b8ac63 for a full test report.

[boegel]

@boegelbot please test @ jsc-zen2
EB_ARGS="ncbi-vdb-2.11.2-gompi-2021b.eb HISAT2-2.2.1-gompi-2021b.eb SKESA-2.4.0-gompi-2021b_saute.1.3.0_1.eb shovill-1.1.0-gompi-2021b.eb"
CORE_CNT=16

[boegelbot]

@boegel: Request for testing this PR well received on jsczen2l1.int.jsc-zen2.easybuild-test.cluster

PR test command 'EB_PR=18236 EB_ARGS="ncbi-vdb-2.11.2-gompi-2021b.eb HISAT2-2.2.1-gompi-2021b.eb SKESA-2.4.0-gompi-2021b_saute.1.3.0_1.eb shovill-1.1.0-gompi-2021b.eb" /opt/software/slurm/bin/sbatch --mem-per-cpu=4000M --job-name test_PR_18236 --ntasks="16" ~/boegelbot/eb_from_pr_upload_jsc-zen2.sh' executed!

• exit code: 0
• output:

Submitted batch job 2921

Test results coming soon (I hope)...

- notification for comment with ID 1613528242 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).

[branfosj]

Test report by @branfosj
FAILED
Build succeeded for 18 out of 20 (4 easyconfigs in total)
bear-pg0105u03a.bear.cluster - Linux RHEL 8.6, x86_64, Intel(R) Xeon(R) Platinum 8360Y CPU @ 2.40GHz (icelake), Python 3.6.8
See https://gist.github.com/branfosj/6f3215095c9345dbcdb91de36e195142 for a full test report.

[boegelbot]

Test report by @boegelbot
FAILED
Build succeeded for 7 out of 9 (4 easyconfigs in total)
jsczen2c1.int.jsc-zen2.easybuild-test.cluster - Linux Rocky Linux 8.5, x86_64, AMD EPYC 7742 64-Core Processor (zen2), Python 3.6.8
See https://gist.github.com/boegelbot/685128cc2af2ea9f2ba420840ee092dc for a full test report.

[branfosj]

Test report by @branfosj
SUCCESS
Build succeeded for 4 out of 4 (4 easyconfigs in total)
bear-pg0105u03a.bear.cluster - Linux RHEL 8.6, x86_64, Intel(R) Xeon(R) Platinum 8360Y CPU @ 2.40GHz (icelake), Python 3.6.8
See https://gist.github.com/branfosj/43599b085973a0e0b89a1d354c2dfc50 for a full test report.

[branfosj]

@boegelbot please test @ jsc-zen2
EB_ARGS="ncbi-vdb-2.11.2-gompi-2021b.eb HISAT2-2.2.1-gompi-2021b.eb SKESA-2.4.0-gompi-2021b_saute.1.3.0_1.eb shovill-1.1.0-gompi-2021b.eb"
CORE_CNT=16

[boegelbot]

@branfosj: Request for testing this PR well received on jsczen2l1.int.jsc-zen2.easybuild-test.cluster

PR test command 'EB_PR=18236 EB_ARGS="ncbi-vdb-2.11.2-gompi-2021b.eb HISAT2-2.2.1-gompi-2021b.eb SKESA-2.4.0-gompi-2021b_saute.1.3.0_1.eb shovill-1.1.0-gompi-2021b.eb" /opt/software/slurm/bin/sbatch --mem-per-cpu=4000M --job-name test_PR_18236 --ntasks="16" ~/boegelbot/eb_from_pr_upload_jsc-zen2.sh' executed!

• exit code: 0
• output:

Submitted batch job 2923

Test results coming soon (I hope)...

- notification for comment with ID 1613572746 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).

[branfosj]

#18237 for fixing the Velvet source download

[boegelbot]

Test report by @boegelbot
SUCCESS
Build succeeded for 4 out of 4 (4 easyconfigs in total)
jsczen2c1.int.jsc-zen2.easybuild-test.cluster - Linux Rocky Linux 8.5, x86_64, AMD EPYC 7742 64-Core Processor (zen2), Python 3.6.8
See https://gist.github.com/boegelbot/0bb14da9dcfb118e01c9c7a88e526ae7 for a full test report.

[branfosj]

Going in, thanks @boegel!