Add easyconfig Bowtie2-2.5.1-GCC-13.2.0.eb

[julianmorillo]

No description provided.

[github-actions]

Updated software Bowtie2-2.5.4-GCC-13.2.0.eb

Diff against Bowtie2-2.5.1-GCC-10.3.0.eb

easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.5.1-GCC-10.3.0.eb

diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.5.1-GCC-10.3.0.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.5.4-GCC-13.2.0.eb
index b8a6bb8555..a4747a3803 100644
--- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.5.1-GCC-10.3.0.eb
+++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.5.4-GCC-13.2.0.eb
@@ -11,9 +11,7 @@
 # SIB Swiss Institute of Bioinformatics
 
 name = 'Bowtie2'
-version = '2.5.1'
-_simde_version = '20220504'
-_simde_commit = 'cbef1c1'
+version = '2.5.4'
 
 homepage = 'https://bowtie-bio.sourceforge.net/bowtie2/index.shtml'
 description = """ Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads
@@ -22,33 +20,33 @@ description = """ Bowtie 2 is an ultrafast and memory-efficient tool for alignin
  Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome,
  its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes."""
 
-toolchain = {'name': 'GCC', 'version': '10.3.0'}
+toolchain = {'name': 'GCC', 'version': '13.2.0'}
 toolchainopts = {'pic': True, 'cstd': 'gnu++98'}
 
 source_urls = [('https://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')]
 sources = ['%(namelower)s-%(version)s-source.zip']
-checksums = ['cb6cbbbb5a7167a2f21a3d63cb9774336361f540e1ec3d8ff907f955c35f71b8']
-
-# SIMD Everywhere implementations only, for non-x86_64 systems
-if ARCH != 'x86_64':
-    source_urls += ['https://github.com/simd-everywhere/simde-no-tests/archive']
-    sources += [
-        {'download_filename': '%s.zip' % _simde_commit,
-         'filename': 'simde-%s.zip' % _simde_version,
-         'extract_cmd': 'unzip %%s && mv simde*-%s*/* %%(namelower)s-%%(version)s/third_party/simde/' % _simde_commit,
-         }
-    ]
-    checksums += ['d01f084ef5ff69b0a9b96370ae314fe1e55ef3339b25afcd3385958ac0e6ad68']
+patches = [
+    'Bowtie2-2.5.4-GCC-13.2.0-riscv.patch',
+    'Bowtie2-2.5.4-GCC-13.2.0-riscv-sse_wrap.patch',]
+checksums = [
+    {'%(namelower)s-%(version)s-source.zip': '94ec207a0494b9f5e0e62dbbca8cb79fe4ff16602395802a86d098349c6ef004'},
+    {'Bowtie2-2.5.4-GCC-13.2.0-riscv.patch': 'e39820af3d0eba9346e6a15d94a0b45552736c62ab8648c2f92ed05272fd96af'},
+    {'Bowtie2-2.5.4-GCC-13.2.0-riscv-sse_wrap.patch': '4bffde4d07a5f2db24bb5f723c408e27c3156443e7c2c1f297daa59d4638b437'},
+]
 
 dependencies = [
-    ('zlib', '1.2.11'),
-    ('Perl', '5.32.1'),
-    ('Python', '3.9.5'),
+    ('zlib', '1.2.13'),
+    ('Perl', '5.38.0'),
+    ('Python', '3.12.3'),
 ]
 
+
 # to add script folder to path just uncomment this line
 # modextrapaths = {'PATH': 'scripts'}
 
-sanity_check_commands = ['bowtie2 --help', 'bowtie2-build --help']
+sanity_check_commands = [
+    "%(namelower)s --help",
+    "%(namelower)s-build --help",
+]
 
 moduleclass = 'bio'

Diff against Bowtie2-2.5.1-GCC-12.3.0.eb

easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.5.1-GCC-12.3.0.eb

diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.5.1-GCC-12.3.0.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.5.4-GCC-13.2.0.eb
index 379484dfae..a4747a3803 100644
--- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.5.1-GCC-12.3.0.eb
+++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.5.4-GCC-13.2.0.eb
@@ -11,7 +11,7 @@
 # SIB Swiss Institute of Bioinformatics
 
 name = 'Bowtie2'
-version = '2.5.1'
+version = '2.5.4'
 
 homepage = 'https://bowtie-bio.sourceforge.net/bowtie2/index.shtml'
 description = """ Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads
@@ -20,17 +20,24 @@ description = """ Bowtie 2 is an ultrafast and memory-efficient tool for alignin
  Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome,
  its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes."""
 
-toolchain = {'name': 'GCC', 'version': '12.3.0'}
+toolchain = {'name': 'GCC', 'version': '13.2.0'}
 toolchainopts = {'pic': True, 'cstd': 'gnu++98'}
 
 source_urls = [('https://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')]
 sources = ['%(namelower)s-%(version)s-source.zip']
-checksums = ['cb6cbbbb5a7167a2f21a3d63cb9774336361f540e1ec3d8ff907f955c35f71b8']
+patches = [
+    'Bowtie2-2.5.4-GCC-13.2.0-riscv.patch',
+    'Bowtie2-2.5.4-GCC-13.2.0-riscv-sse_wrap.patch',]
+checksums = [
+    {'%(namelower)s-%(version)s-source.zip': '94ec207a0494b9f5e0e62dbbca8cb79fe4ff16602395802a86d098349c6ef004'},
+    {'Bowtie2-2.5.4-GCC-13.2.0-riscv.patch': 'e39820af3d0eba9346e6a15d94a0b45552736c62ab8648c2f92ed05272fd96af'},
+    {'Bowtie2-2.5.4-GCC-13.2.0-riscv-sse_wrap.patch': '4bffde4d07a5f2db24bb5f723c408e27c3156443e7c2c1f297daa59d4638b437'},
+]
 
 dependencies = [
     ('zlib', '1.2.13'),
-    ('Perl', '5.36.1'),
-    ('Python', '3.11.3'),
+    ('Perl', '5.38.0'),
+    ('Python', '3.12.3'),
 ]
 
 

Diff against Bowtie2-2.5.1-GCC-12.2.0.eb

easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.5.1-GCC-12.2.0.eb

diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.5.1-GCC-12.2.0.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.5.4-GCC-13.2.0.eb
index 54650aff98..a4747a3803 100644
--- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.5.1-GCC-12.2.0.eb
+++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.5.4-GCC-13.2.0.eb
@@ -11,9 +11,7 @@
 # SIB Swiss Institute of Bioinformatics
 
 name = 'Bowtie2'
-version = '2.5.1'
-_simde_version = '20220504'
-_simde_commit = 'cbef1c1'
+version = '2.5.4'
 
 homepage = 'https://bowtie-bio.sourceforge.net/bowtie2/index.shtml'
 description = """ Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads
@@ -22,33 +20,33 @@ description = """ Bowtie 2 is an ultrafast and memory-efficient tool for alignin
  Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome,
  its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes."""
 
-toolchain = {'name': 'GCC', 'version': '12.2.0'}
+toolchain = {'name': 'GCC', 'version': '13.2.0'}
 toolchainopts = {'pic': True, 'cstd': 'gnu++98'}
 
 source_urls = [('https://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')]
 sources = ['%(namelower)s-%(version)s-source.zip']
-checksums = ['cb6cbbbb5a7167a2f21a3d63cb9774336361f540e1ec3d8ff907f955c35f71b8']
-
-# SIMD Everywhere implementations only, for non-x86_64 systems
-if ARCH != 'x86_64':
-    source_urls += ['https://github.com/simd-everywhere/simde-no-tests/archive']
-    sources += [
-        {'download_filename': '%s.zip' % _simde_commit,
-         'filename': 'simde-%s.zip' % _simde_version,
-         'extract_cmd': 'unzip %%s && mv simde*-%s*/* %%(namelower)s-%%(version)s/third_party/simde/' % _simde_commit,
-         }
-    ]
-    checksums += ['d01f084ef5ff69b0a9b96370ae314fe1e55ef3339b25afcd3385958ac0e6ad68']
+patches = [
+    'Bowtie2-2.5.4-GCC-13.2.0-riscv.patch',
+    'Bowtie2-2.5.4-GCC-13.2.0-riscv-sse_wrap.patch',]
+checksums = [
+    {'%(namelower)s-%(version)s-source.zip': '94ec207a0494b9f5e0e62dbbca8cb79fe4ff16602395802a86d098349c6ef004'},
+    {'Bowtie2-2.5.4-GCC-13.2.0-riscv.patch': 'e39820af3d0eba9346e6a15d94a0b45552736c62ab8648c2f92ed05272fd96af'},
+    {'Bowtie2-2.5.4-GCC-13.2.0-riscv-sse_wrap.patch': '4bffde4d07a5f2db24bb5f723c408e27c3156443e7c2c1f297daa59d4638b437'},
+]
 
 dependencies = [
-    ('zlib', '1.2.12'),
-    ('Perl', '5.36.0'),
-    ('Python', '3.10.8'),
+    ('zlib', '1.2.13'),
+    ('Perl', '5.38.0'),
+    ('Python', '3.12.3'),
 ]
 
+
 # to add script folder to path just uncomment this line
 # modextrapaths = {'PATH': 'scripts'}
 
-sanity_check_commands = ['bowtie2 --help', 'bowtie2-build --help']
+sanity_check_commands = [
+    "%(namelower)s --help",
+    "%(namelower)s-build --help",
+]
 
 moduleclass = 'bio'