Add Mothur 1.48.2 for foss-2023b #21857

jgustavsen · 2024-11-15T12:04:10Z

Hello,
Thanks to the help of @Micket, this is an attempt to resolve #21849.

This is my first PR for Easybuild and happy to adapt as much as needed if this is a helpful addition.
Thanks, Julia

github-actions · 2024-11-15T12:04:43Z

Updated software `Mothur-1.48.2-foss-2023b.eb`

Diff against Mothur-1.43.0-foss-2019a-Python-3.7.2.eb

easybuild/easyconfigs/m/Mothur/Mothur-1.43.0-foss-2019a-Python-3.7.2.eb

diff --git a/easybuild/easyconfigs/m/Mothur/Mothur-1.43.0-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/m/Mothur/Mothur-1.48.2-foss-2023b.eb
index 16d5db6c6e..2dfa6e10da 100644
--- a/easybuild/easyconfigs/m/Mothur/Mothur-1.43.0-foss-2019a-Python-3.7.2.eb
+++ b/easybuild/easyconfigs/m/Mothur/Mothur-1.48.2-foss-2023b.eb
@@ -1,35 +1,28 @@
-##
-# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia
-# Homepage: 	https://staff.flinders.edu.au/research/deep-thought
-#
-# Authors::	Robert Qiao <[email protected]>
-# License::	GPLv3.0
-#
-# Notes::
-##
-
 name = 'Mothur'
-version = '1.43.0'
-versionsuffix = '-Python-%(pyver)s'
+version = '1.48.2'
 
 homepage = 'https://www.mothur.org/'
 description = """Mothur is a single piece of open-source, expandable software
  to fill the bioinformatics needs of the microbial ecology community."""
 
-toolchain = {'name': 'foss', 'version': '2019a'}
+toolchain = {'name': 'foss', 'version': '2023b'}
 toolchainopts = {'usempi': True, 'cstd': 'c++11'}
 
 source_urls = ['https://github.com/mothur/mothur/archive/']
 sources = ['v%(version)s.tar.gz']
-checksums = ['12ccd95a85bec3bb1564b8feabd244ea85413973740754803d01fc71ecb0a2c1']
+patches = ['Mothur-%(version)s_fix-hardcoding.patch']
+checksums = [
+    {'v1.48.2.tar.gz': 'bd37b22b5d2629c5f44bd7f104c5e5a2c3a117d724cd113ec7526c4aa62e1793'},
+    {'Mothur-1.48.2_fix-hardcoding.patch': 'a3b3524909c77fb8b6dbecd979debcaadab21637757430f99f3f6b4a966c470a'},
+]
 
 dependencies = [
-    ('Python', '3.7.2'),
-    ('Boost.Python', '1.70.0', '', ('gompi', '2019a')),
-    ('HDF5', '1.10.5', '', ('gompi', '2019a')),
-    ('libreadline', '8.0', '', ('GCCcore', '8.2.0')),
-    ('ncurses', '6.1', '', ('GCCcore', '8.2.0')),
-    ('zlib', '1.2.11'),
+    ('Python', '3.11.5'),
+    ('Boost.Python', '1.83.0'),
+    ('HDF5', '1.14.3'),
+    ('libreadline', '8.2'),
+    ('ncurses', '6.4'),
+    ('zlib', '1.2.13'),
 ]
 
 moduleclass = 'bio'

Diff against Mothur-1.41.0-foss-2018b-Python-2.7.15.eb

easybuild/easyconfigs/m/Mothur/Mothur-1.41.0-foss-2018b-Python-2.7.15.eb

diff --git a/easybuild/easyconfigs/m/Mothur/Mothur-1.41.0-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/m/Mothur/Mothur-1.48.2-foss-2023b.eb
index f65fe180be..2dfa6e10da 100644
--- a/easybuild/easyconfigs/m/Mothur/Mothur-1.41.0-foss-2018b-Python-2.7.15.eb
+++ b/easybuild/easyconfigs/m/Mothur/Mothur-1.48.2-foss-2023b.eb
@@ -1,29 +1,28 @@
 name = 'Mothur'
-version = '1.41.0'
-versionsuffix = '-Python-%(pyver)s'
+version = '1.48.2'
 
-homepage = 'http://www.mothur.org/'
+homepage = 'https://www.mothur.org/'
 description = """Mothur is a single piece of open-source, expandable software
  to fill the bioinformatics needs of the microbial ecology community."""
 
-toolchain = {'name': 'foss', 'version': '2018b'}
+toolchain = {'name': 'foss', 'version': '2023b'}
 toolchainopts = {'usempi': True, 'cstd': 'c++11'}
 
 source_urls = ['https://github.com/mothur/mothur/archive/']
 sources = ['v%(version)s.tar.gz']
 patches = ['Mothur-%(version)s_fix-hardcoding.patch']
 checksums = [
-    'b54b71e46f96ff2604ba8e3b33f95c067e6921cbb212b603365e6483d05574f1',  # v1.41.0.tar.gz
-    'f270fcf19bcd494189c7b977141d3f6b96546b426d7d351d1696b77e85e0d3fa',  # Mothur-1.41.0_fix-hardcoding.patch
+    {'v1.48.2.tar.gz': 'bd37b22b5d2629c5f44bd7f104c5e5a2c3a117d724cd113ec7526c4aa62e1793'},
+    {'Mothur-1.48.2_fix-hardcoding.patch': 'a3b3524909c77fb8b6dbecd979debcaadab21637757430f99f3f6b4a966c470a'},
 ]
 
 dependencies = [
-    ('Python', '2.7.15'),
-    ('Boost.Python', '1.67.0', versionsuffix),
-    ('HDF5', '1.10.2'),
-    ('libreadline', '7.0'),
-    ('ncurses', '6.1'),
-    ('zlib', '1.2.11'),
+    ('Python', '3.11.5'),
+    ('Boost.Python', '1.83.0'),
+    ('HDF5', '1.14.3'),
+    ('libreadline', '8.2'),
+    ('ncurses', '6.4'),
+    ('zlib', '1.2.13'),
 ]
 
 moduleclass = 'bio'

Diff against Mothur-1.39.5-intel-2017a-Python-2.7.13.eb

easybuild/easyconfigs/m/Mothur/Mothur-1.39.5-intel-2017a-Python-2.7.13.eb

diff --git a/easybuild/easyconfigs/m/Mothur/Mothur-1.39.5-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/m/Mothur/Mothur-1.48.2-foss-2023b.eb
index 07729f03aa..2dfa6e10da 100644
--- a/easybuild/easyconfigs/m/Mothur/Mothur-1.39.5-intel-2017a-Python-2.7.13.eb
+++ b/easybuild/easyconfigs/m/Mothur/Mothur-1.48.2-foss-2023b.eb
@@ -1,30 +1,28 @@
 name = 'Mothur'
-version = '1.39.5'
-versionsuffix = '-Python-%(pyver)s'
+version = '1.48.2'
 
-homepage = 'http://www.mothur.org/'
+homepage = 'https://www.mothur.org/'
 description = """Mothur is a single piece of open-source, expandable software
  to fill the bioinformatics needs of the microbial ecology community."""
 
-toolchain = {'name': 'intel', 'version': '2017a'}
-toolchainopts = {'usempi': True, 'cstd': 'c++0x'}
+toolchain = {'name': 'foss', 'version': '2023b'}
+toolchainopts = {'usempi': True, 'cstd': 'c++11'}
 
 source_urls = ['https://github.com/mothur/mothur/archive/']
 sources = ['v%(version)s.tar.gz']
 patches = ['Mothur-%(version)s_fix-hardcoding.patch']
 checksums = [
-    '9f1cd691e9631a2ab7647b19eb59cd21ea643f29b22cde73d7f343372dfee342',  # v1.39.5.tar.gz
-    '64ca39179acbcf6c3071369b4689e5bbbeb8cf0b5a0cbe10a8c6bef6c29936ba',  # Mothur-1.39.5_fix-hardcoding.patch
+    {'v1.48.2.tar.gz': 'bd37b22b5d2629c5f44bd7f104c5e5a2c3a117d724cd113ec7526c4aa62e1793'},
+    {'Mothur-1.48.2_fix-hardcoding.patch': 'a3b3524909c77fb8b6dbecd979debcaadab21637757430f99f3f6b4a966c470a'},
 ]
 
 dependencies = [
-    ('Python', '2.7.13'),
-    ('Boost', '1.65.1', versionsuffix),
-    ('libreadline', '7.0'),
-    ('ncurses', '6.0'),
-    ('bzip2', '1.0.6'),
-    ('gzip', '1.8'),
-    ('zlib', '1.2.11'),
+    ('Python', '3.11.5'),
+    ('Boost.Python', '1.83.0'),
+    ('HDF5', '1.14.3'),
+    ('libreadline', '8.2'),
+    ('ncurses', '6.4'),
+    ('zlib', '1.2.13'),
 ]
 
 moduleclass = 'bio'

Micket · 2024-11-15T12:46:55Z

easybuild/easyconfigs/m/Mothur/Mothur-1.48.2_fix-hardcoding.patch

@@ -0,0 +1,118 @@
+diff -ruN mothur-1.48.2.orig/Makefile /tmp/eb/Mothur/1.48.2/foss-2023b/mothur-1.48.2/Makefile


We ask that patches include a short description what it solves and their author for reference.

Once you include this, please also include the checksum for the patch in the easyconfig.

You can use EB to inject the checksums automatically using

eb Mothur-1.48.2-foss-2023b.eb --inject-checksums

Thanks for the review. I added these in 6f09ef8 and 90fa0d9.

Micket · 2024-11-15T13:02:40Z

easybuild/easyconfigs/m/Mothur/Mothur-1.48.2_fix-hardcoding.patch

+ # MOTHUR_FILES - The MOTHUR_FILES parameter is optional, but allows you to set a default location for mothur to look for input files it can't find. This is often used for reference files you want to store in one location separate from your data.
+
+-INSTALL_DIR ?= "\"Enter_your_mothur_install_path_here\""
+INSTALL_DIR ?= "%(installdir)s"


Hm, is this tested to work? I don't see how it could, the %(installdir)s templates are not applied to patches.

Looking at the custom easyblock that this thing unfortunately needs to use, it's just manually making the installation via copying files, so I this probably doesn't even have any impact.

I was having problems getting the install to work without this change. Before changing this I was getting "undefined reference to main" and others as errors.
So if I understand what you are saying it would mean that I am just setting this to empty and thus could try like in the "MOTHUR_FILES" variable?

Micket · 2024-11-15T13:03:34Z

easybuild/easyconfigs/m/Mothur/Mothur-1.48.2_fix-hardcoding.patch

+     OBJECTS+=$(patsubst %.cpp,%.o,$(wildcard *.cpp))
+     OBJECTS+=$(patsubst %.c,%.o,$(wildcard *.c))
+
+Binary files mothur-1.48.2.orig/source/calculators/prng.o and /tmp/eb/Mothur/1.48.2/foss-2023b/mothur-1.48.2/source/calculators/prng.o differ


this looks like something that shouldn't be included in the patch

Ok thanks, updated here: 6104290

Micket · 2024-11-15T13:05:23Z

easybuild/easyconfigs/m/Mothur/Mothur-1.48.2_fix-hardcoding.patch

+++ /tmp/eb/Mothur/1.48.2/foss-2023b/mothur-1.48.2/source/uchime_src/makefile	2024-11-15 10:29:38.800547895 +0100
+@@ -1,4 +1,4 @@
+-CXXFLAGS = -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1
+CXXFLAGS = -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 -std=c++11


Hm, i wonder if we can just make this add the -D flags instead of overwriting CXXFLAGS completely, so that it catches the EB environment variables which set compiler flags (though I'm not going to insist of it in any way gets tricky).

Very sorry, but I'm not sure how to do this. This would be in the .eb file? thanks

jgustavsen added 2 commits November 15, 2024 12:59

added Mothur 1.48.2 for foss2023b eb file

c3330e2

add patch file for Mothur 1.48.2

ca2b7bd

github-actions bot added the update label Nov 15, 2024

Micket requested changes Nov 15, 2024

View reviewed changes

jgustavsen added 3 commits November 15, 2024 14:24

add author and description to mothur 1.48.2 patch file

6f09ef8

inject checksums into Mothur 1.48.2 eb file

90fa0d9

updated Mothur 1.48.2 patch to remove binary file comparison

6104290

jgustavsen requested a review from Micket November 18, 2024 12:23

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Add Mothur 1.48.2 for foss-2023b #21857

Add Mothur 1.48.2 for foss-2023b #21857

jgustavsen commented Nov 15, 2024

github-actions bot commented Nov 15, 2024 •

edited

Loading

Micket Nov 15, 2024

jgustavsen Nov 15, 2024

Micket Nov 15, 2024

jgustavsen Nov 15, 2024

Micket Nov 15, 2024

jgustavsen Nov 15, 2024

Micket Nov 15, 2024

jgustavsen Nov 15, 2024

		@@ -0,0 +1,118 @@
		diff -ruN mothur-1.48.2.orig/Makefile /tmp/eb/Mothur/1.48.2/foss-2023b/mothur-1.48.2/Makefile

Add Mothur 1.48.2 for foss-2023b #21857

Are you sure you want to change the base?

Add Mothur 1.48.2 for foss-2023b #21857

Conversation

jgustavsen commented Nov 15, 2024

github-actions bot commented Nov 15, 2024 • edited Loading

Updated software Mothur-1.48.2-foss-2023b.eb

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

github-actions bot commented Nov 15, 2024 •

edited

Loading

Updated software `Mothur-1.48.2-foss-2023b.eb`