Skip to content

{bio}[GCCcore/12.3.0,foss/2023a] MitoFinder v1.4.2, IDBA-UD v1.1.3 w/ Python 2.7.18#22017

Merged
verdurin merged 1 commit intoeasybuilders:developfrom
pavelToman:20241212145119_new_pr_MitoFinder142
Dec 18, 2024
Merged

{bio}[GCCcore/12.3.0,foss/2023a] MitoFinder v1.4.2, IDBA-UD v1.1.3 w/ Python 2.7.18#22017
verdurin merged 1 commit intoeasybuilders:developfrom
pavelToman:20241212145119_new_pr_MitoFinder142

Conversation

@pavelToman
Copy link
Copy Markdown
Collaborator

@pavelToman pavelToman commented Dec 12, 2024

(created using eb --new-pr)
resolves vscentrum/vsc-software-stack#216

@github-actions
Copy link
Copy Markdown

Updated software IDBA-UD-1.1.3-GCCcore-12.3.0.eb

Diff against IDBA-UD-1.1.3-GCC-10.3.0.eb

easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.3-GCC-10.3.0.eb

diff --git a/easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.3-GCC-10.3.0.eb b/easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.3-GCCcore-12.3.0.eb
index 6b69859e25..83d24a82ee 100644
--- a/easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.3-GCC-10.3.0.eb
+++ b/easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.3-GCCcore-12.3.0.eb
@@ -24,12 +24,14 @@ locally to generate some missing k-mers in low-depth regions. With these technol
 can iterate k value of de Bruijn graph to a very large value with less gaps and less branches
 to form long contigs in both low-depth and high-depth regions."""
 
-toolchain = {'name': 'GCC', 'version': '10.3.0'}
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
 
 source_urls = ['https://github.com/loneknightpy/idba/releases/download/%(version)s']
 sources = ['idba-%(version)s.tar.gz']
 checksums = ['030e24463c6d725c1c202baabf773b605b51e310844fd0f27f4688ecfbae26d0']
 
+builddependencies = [('binutils', '2.40')]
+
 prebuildopts = './configure && '
 
 # we delete every .o and Makefile file which is left in bin folder
Diff against IDBA-UD-1.1.3-GCC-11.2.0.eb

easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.3-GCC-11.2.0.eb

diff --git a/easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.3-GCC-11.2.0.eb b/easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.3-GCCcore-12.3.0.eb
index 8d4d05d646..83d24a82ee 100644
--- a/easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.3-GCC-11.2.0.eb
+++ b/easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.3-GCCcore-12.3.0.eb
@@ -24,12 +24,14 @@ locally to generate some missing k-mers in low-depth regions. With these technol
 can iterate k value of de Bruijn graph to a very large value with less gaps and less branches
 to form long contigs in both low-depth and high-depth regions."""
 
-toolchain = {'name': 'GCC', 'version': '11.2.0'}
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
 
 source_urls = ['https://github.com/loneknightpy/idba/releases/download/%(version)s']
 sources = ['idba-%(version)s.tar.gz']
 checksums = ['030e24463c6d725c1c202baabf773b605b51e310844fd0f27f4688ecfbae26d0']
 
+builddependencies = [('binutils', '2.40')]
+
 prebuildopts = './configure && '
 
 # we delete every .o and Makefile file which is left in bin folder
Diff against IDBA-UD-1.1.3-GCC-9.3.0.eb

easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.3-GCC-9.3.0.eb

diff --git a/easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.3-GCC-9.3.0.eb b/easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.3-GCCcore-12.3.0.eb
index 4ef50bfe52..83d24a82ee 100644
--- a/easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.3-GCC-9.3.0.eb
+++ b/easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.3-GCCcore-12.3.0.eb
@@ -16,20 +16,22 @@ version = '1.1.3'
 
 homepage = 'https://i.cs.hku.hk/~alse/hkubrg/projects/idba_ud/'
 description = """ IDBA-UD is a iterative De Bruijn Graph De Novo Assembler for Short Reads
- Sequencing data with Highly Uneven Sequencing Depth. It is an extension of IDBA algorithm.
- IDBA-UD also iterates from small k to a large k. In each iteration, short and low-depth
- contigs are removed iteratively with cutoff threshold from low to high to reduce the errors
- in low-depth and high-depth regions. Paired-end reads are aligned to contigs and assembled
- locally to generate some missing k-mers in low-depth regions. With these technologies, IDBA-UD
- can iterate k value of de Bruijn graph to a very large value with less gaps and less branches
- to form long contigs in both low-depth and high-depth regions."""
+Sequencing data with Highly Uneven Sequencing Depth. It is an extension of IDBA algorithm.
+IDBA-UD also iterates from small k to a large k. In each iteration, short and low-depth
+contigs are removed iteratively with cutoff threshold from low to high to reduce the errors
+in low-depth and high-depth regions. Paired-end reads are aligned to contigs and assembled
+locally to generate some missing k-mers in low-depth regions. With these technologies, IDBA-UD
+can iterate k value of de Bruijn graph to a very large value with less gaps and less branches
+to form long contigs in both low-depth and high-depth regions."""
 
-toolchain = {'name': 'GCC', 'version': '9.3.0'}
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
 
 source_urls = ['https://github.com/loneknightpy/idba/releases/download/%(version)s']
 sources = ['idba-%(version)s.tar.gz']
 checksums = ['030e24463c6d725c1c202baabf773b605b51e310844fd0f27f4688ecfbae26d0']
 
+builddependencies = [('binutils', '2.40')]
+
 prebuildopts = './configure && '
 
 # we delete every .o and Makefile file which is left in bin folder

@pavelToman
Copy link
Copy Markdown
Collaborator Author

@boegelbot please test @ generoso

@boegelbot
Copy link
Copy Markdown
Collaborator

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

PR test command 'EB_PR=22017 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_22017 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

  • exit code: 0
  • output:
Submitted batch job 14860

Test results coming soon (I hope)...

Details

- notification for comment with ID 2539022447 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).

@pavelToman
Copy link
Copy Markdown
Collaborator Author

Test report by @pavelToman
SUCCESS
Build succeeded for 2 out of 2 (2 easyconfigs in total)
node4008.donphan.os - Linux RHEL 8.8, x86_64, Intel(R) Xeon(R) Gold 6240 CPU @ 2.60GHz, 1 x NVIDIA NVIDIA A2, 545.23.08, Python 3.6.8
See https://gist.github.com/pavelToman/fec8e6f9999bc17ee283d1558b4b1268 for a full test report.

@boegelbot
Copy link
Copy Markdown
Collaborator

Test report by @boegelbot
SUCCESS
Build succeeded for 2 out of 2 (2 easyconfigs in total)
cns1 - Linux Rocky Linux 8.9, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/boegelbot/e5e07ef5384481f8acae2155070d4623 for a full test report.

@pavelToman
Copy link
Copy Markdown
Collaborator Author

@boegelbot please test @ jsc-zen3

@pavelToman
Copy link
Copy Markdown
Collaborator Author

Test report by @pavelToman
SUCCESS
Build succeeded for 2 out of 2 (2 easyconfigs in total)
node4203.shinx.os - Linux RHEL 9.4, x86_64, AMD EPYC 9654 96-Core Processor, Python 3.9.18
See https://gist.github.com/pavelToman/171cca665060ad3cf644bcd8542298e9 for a full test report.

@boegelbot
Copy link
Copy Markdown
Collaborator

@pavelToman: Request for testing this PR well received on jsczen3l1.int.jsc-zen3.fz-juelich.de

PR test command 'if [[ develop != 'develop' ]]; then EB_BRANCH=develop ./easybuild_develop.sh 2> /dev/null 1>&2; EB_PREFIX=/home/boegelbot/easybuild/develop source init_env_easybuild_develop.sh; fi; EB_PR=22017 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_22017 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

  • exit code: 0
  • output:
Submitted batch job 5432

Test results coming soon (I hope)...

Details

- notification for comment with ID 2539037887 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
Copy link
Copy Markdown
Collaborator

Test report by @boegelbot
SUCCESS
Build succeeded for 2 out of 2 (2 easyconfigs in total)
jsczen3c1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.5, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.19
See https://gist.github.com/boegelbot/2c1e71020539352003ca2b6d76924a3b for a full test report.

@verdurin
Copy link
Copy Markdown
Member

Test report by @verdurin
SUCCESS
Build succeeded for 4 out of 4 (2 easyconfigs in total)
easybuild-el8.cloud.in.bmrc.ox.ac.uk - Linux Rocky Linux 8.10, x86_64, Intel Xeon Processor (Skylake, IBRS), Python 3.6.8
See https://gist.github.com/verdurin/95d94b933f7fb8f394fac4a8f1f803bf for a full test report.

Copy link
Copy Markdown
Member

@verdurin verdurin left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Looks fine.

@verdurin verdurin added this to the release after 4.9.4 milestone Dec 18, 2024
@verdurin
Copy link
Copy Markdown
Member

Going in, thanks @pavelToman!

@verdurin verdurin merged commit e406a5e into easybuilders:develop Dec 18, 2024
@boegel boegel modified the milestones: release after 4.9.4, 5.0.0 Mar 18, 2025
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Projects

None yet

Development

Successfully merging this pull request may close these issues.

MitoFinder

4 participants