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{bio}[gompi/2023a] IQ-TREE v2.3.6 #21883

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{bio}[gompi/2023a] IQ-TREE v2.3.6 #21883

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PetrKralCZ
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@PetrKralCZ PetrKralCZ commented Nov 19, 2024 •
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(created using eb --new-pr)
resolves vscentrum/vsc-software-stack#459

@PetrKralCZ PetrKralCZ mentioned this pull request Nov 19, 2024
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Updated software IQ-TREE-2.3.6-gompi-2023a.eb

Diff against IQ-TREE-2.3.5-gompi-2023a.eb

easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.3.5-gompi-2023a.eb

diff --git a/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.3.5-gompi-2023a.eb b/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.3.6-gompi-2023a.eb
index ca4c707da6..7f78472bce 100644
--- a/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.3.5-gompi-2023a.eb
+++ b/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.3.6-gompi-2023a.eb
@@ -1,11 +1,12 @@
 # Updated to v2.1.3 by
 # R.QIAO <[email protected]>
 # DeepThought, Flinders University
+# Update: Petr Král (INUITS)
 
 easyblock = 'CMakeMake'
 
 name = 'IQ-TREE'
-version = '2.3.5'
+version = '2.3.6'
 
 # HTTPS is not working
 homepage = 'http://www.iqtree.org/'
@@ -20,7 +21,7 @@ patches = [
     'IQ-TREE-2.3.5_use_EB_LSD2.patch',
 ]
 checksums = [
-    {'v2.3.5.tar.gz': '8e323e0b7c46e97901d3500f11e810703e0e5d25848188047eca9602d03fa6b1'},
+    {'v2.3.6.tar.gz': '2d389ea74e19773496363cd68270b341ac7cc47c60e7f32859682403b34744cf'},
     {'IQ-TREE-2.3.5_use_EB_LSD2.patch': 'b4578b01f06ae52b94b332622c0f6630497cd29cb61010f58f7c5018c2c32a5f'},
 ]
Diff against IQ-TREE-2.2.2.7-gompi-2023a.eb

easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.2.2.7-gompi-2023a.eb

diff --git a/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.2.2.7-gompi-2023a.eb b/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.3.6-gompi-2023a.eb
index eeb8368751..7f78472bce 100644
--- a/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.2.2.7-gompi-2023a.eb
+++ b/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.3.6-gompi-2023a.eb
@@ -1,11 +1,12 @@
 # Updated to v2.1.3 by
 # R.QIAO <[email protected]>
 # DeepThought, Flinders University
+# Update: Petr Král (INUITS)
 
 easyblock = 'CMakeMake'
 
 name = 'IQ-TREE'
-version = '2.2.2.7'
+version = '2.3.6'
 
 # HTTPS is not working
 homepage = 'http://www.iqtree.org/'
@@ -14,16 +15,14 @@ description = """Efficient phylogenomic software by maximum likelihood"""
 toolchain = {'name': 'gompi', 'version': '2023a'}
 # Including 'usempi' will take precedence and override IQTREE_FLAGS and produces only 'iqtree-mpi' binary
 
-source_urls = ['https://github.com/iqtree/iqtree2/archive/']
+source_urls = ['https://github.com/iqtree/iqtree2/archive/refs/tags/']
 sources = ['v%(version)s.tar.gz']
 patches = [
-    'IQ-TREE-2.1.2_use_EB_LSD2.patch',
-    'IQ-TREE-2.2.1_fix-mpi.patch',
+    'IQ-TREE-2.3.5_use_EB_LSD2.patch',
 ]
 checksums = [
-    {'v2.2.2.7.tar.gz': '407a1a56d352ba9c2152a1d708cd29db872a41c252fbdc7acd8e0de0da8af008'},
-    {'IQ-TREE-2.1.2_use_EB_LSD2.patch': 'daa2ab12d44e26eb5607c4ed6acb9d970e230a83dabcf21461f37bc48263b816'},
-    {'IQ-TREE-2.2.1_fix-mpi.patch': '9ead6808efd11d4c01dd265cca6094cffd6377746d3b2fc84b43d2faeee0777c'},
+    {'v2.3.6.tar.gz': '2d389ea74e19773496363cd68270b341ac7cc47c60e7f32859682403b34744cf'},
+    {'IQ-TREE-2.3.5_use_EB_LSD2.patch': 'b4578b01f06ae52b94b332622c0f6630497cd29cb61010f58f7c5018c2c32a5f'},
 ]
 
 builddependencies = [
Diff against IQ-TREE-2.2.2.6-gompi-2022b.eb

easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.2.2.6-gompi-2022b.eb

diff --git a/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.2.2.6-gompi-2022b.eb b/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.3.6-gompi-2023a.eb
index bc6834e8e8..7f78472bce 100644
--- a/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.2.2.6-gompi-2022b.eb
+++ b/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.3.6-gompi-2023a.eb
@@ -1,38 +1,37 @@
 # Updated to v2.1.3 by
 # R.QIAO <[email protected]>
 # DeepThought, Flinders University
+# Update: Petr Král (INUITS)
 
 easyblock = 'CMakeMake'
 
 name = 'IQ-TREE'
-version = '2.2.2.6'
+version = '2.3.6'
 
 # HTTPS is not working
 homepage = 'http://www.iqtree.org/'
 description = """Efficient phylogenomic software by maximum likelihood"""
 
-toolchain = {'name': 'gompi', 'version': '2022b'}
+toolchain = {'name': 'gompi', 'version': '2023a'}
 # Including 'usempi' will take precedence and override IQTREE_FLAGS and produces only 'iqtree-mpi' binary
 
-source_urls = ['https://github.com/iqtree/iqtree2/archive/']
+source_urls = ['https://github.com/iqtree/iqtree2/archive/refs/tags/']
 sources = ['v%(version)s.tar.gz']
 patches = [
-    'IQ-TREE-2.1.2_use_EB_LSD2.patch',
-    'IQ-TREE-2.2.1_fix-mpi.patch',
+    'IQ-TREE-2.3.5_use_EB_LSD2.patch',
 ]
 checksums = [
-    {'v2.2.2.6.tar.gz': 'f5d10c033f2ed1c81bb473f572c7a9fe72a275a48e2e93ad74e5f1c3d32fa8b9'},
-    {'IQ-TREE-2.1.2_use_EB_LSD2.patch': 'daa2ab12d44e26eb5607c4ed6acb9d970e230a83dabcf21461f37bc48263b816'},
-    {'IQ-TREE-2.2.1_fix-mpi.patch': '9ead6808efd11d4c01dd265cca6094cffd6377746d3b2fc84b43d2faeee0777c'},
+    {'v2.3.6.tar.gz': '2d389ea74e19773496363cd68270b341ac7cc47c60e7f32859682403b34744cf'},
+    {'IQ-TREE-2.3.5_use_EB_LSD2.patch': 'b4578b01f06ae52b94b332622c0f6630497cd29cb61010f58f7c5018c2c32a5f'},
 ]
 
 builddependencies = [
-    ('CMake', '3.24.3'),
+    ('CMake', '3.26.3'),
     ('Eigen', '3.4.0'),
 ]
 dependencies = [
-    ('zlib', '1.2.12'),
-    ('Boost', '1.81.0'),
+    ('zlib', '1.2.13'),
+    ('Boost', '1.82.0'),
     ('LSD2', '2.4.1'),
 ]

@pavelToman pavelToman mentioned this pull request Nov 19, 2024
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Test report by @verdurin
SUCCESS
Build succeeded for 1 out of 1 (1 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/37afff6d9f93170f21b1a1f4927cb85d for a full test report.

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@boegelbot please test @ generoso

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

PR test command 'EB_PR=21883 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_21883 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

  • exit code: 0
  • output:
Submitted batch job 14782

Test results coming soon (I hope)...

- notification for comment with ID 2507440620 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).

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Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 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/a9e98954ddcba00acfe97d5767553c45 for a full test report.

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@boegelbot please test @ jsc-zen3

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@verdurin: 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=21883 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_21883 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

  • exit code: 0
  • output:
Submitted batch job 5356

Test results coming soon (I hope)...

- notification for comment with ID 2508110082 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).

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Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 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/a90f285bdd0c5c098e5044374f5ef30d for a full test report.

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IQ-TREE 2.3.6
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@PetrKralCZ @verdurin @boegelbot