fix suggestions for ABRA2, CRISPR-DAV, PRINSEQ easyconfigs

easybuilders · Aug 19, 2021 · 47df656 · 47df656
1 parent f231d83
commit 47df656
Show file tree

Hide file tree

Showing 4 changed files with 12 additions and 17 deletions.
diff --git a/easybuild/easyconfigs/a/ABRA2/ABRA2-2.23-GCC-10.2.0.eb b/easybuild/easyconfigs/a/ABRA2/ABRA2-2.23-GCC-10.2.0.eb
@@ -41,8 +41,7 @@ sanity_check_paths = {
     'dirs': [],
 }
 
-modextravars = {
-    "LC_ALL": "en_US.UTF-8",
-}
+# required to work around localization bug, see https://github.com/mozack/abra2/issues/25
+modextravars = {'LC_ALL': 'en_US.UTF-8'}
 
 moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/c/CRISPR-DAV/CRISPR-DAV-2.3.4-foss-2020b.eb b/easybuild/easyconfigs/c/CRISPR-DAV/CRISPR-DAV-2.3.4-foss-2020b.eb
@@ -9,17 +9,15 @@ toolchain = {'name': 'foss', 'version': '2020b'}
 
 source_urls = ['https://github.com/pinetree1/crispr-dav/archive/']
 sources = ['v%(version)s.tar.gz']
-patches = ['crispr-dav-2.3.4_remove_hardcoding.patch']
+patches = ['CRISPR-DAV-%(version)s_remove_hardcoding.patch']
 checksums = [
     '49975cd48bdbf31fe5a9e2aaa3f5ed85d3cc6f65a422ee3aa8daed890159d2ae',  # v2.3.4.tar.gz
     # crispr-dav-2.3.4-foss2020b_remove_hardcoding.patch
     '41475a09754d65cc2c88d4161be6eacdfc98242bccbe49778c4f1f74210a6cb2',
 ]
 
-# also needs `naturalsort`, which is now an R extension - see https://github.com/easybuilders/easybuild-easyconfigs/pull/13762
-# if missing, try reinstalling R (https://docs.easybuild.io/en/latest/Partial_installations.html#installing-additional-extensions-using-k-skip)
 dependencies = [
-    ('R', '4.0.3'),
+    ('R', '4.0.3'),  # provides naturalsort R package
     ('Perl', '5.32.0'),
     ('NGS', '2.10.9'),
     ('Pysam', '0.16.0.1'),

diff --git a/.../crispr-dav-2.3.4_remove_hardcoding.patch → .../CRISPR-DAV-2.3.4_remove_hardcoding.patch b/.../crispr-dav-2.3.4_remove_hardcoding.patch → .../CRISPR-DAV-2.3.4_remove_hardcoding.patch
diff --git a/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2020b-Perl-5.32.0.eb b/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2020b-Perl-5.32.0.eb
@@ -77,23 +77,21 @@ exts_list = [
     }),
 ]
 
-# this is the script which relies in many extra Perl libraries so we verify it's working fine
-sanity_check_commands = ['%(installdir)s/prinseq-graphs.pl']
+fix_perl_shebang_for = ["*.pl"]
 
-modextrapaths = {
-    'PATH': '',
-    'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/',
-}
+postinstallcmds = ["chmod +x %(installdir)s/*.pl"]
 
-postinstallcmds = [
-    "sed -i -e 's|/usr/bin/perl|/usr/bin/env\ perl|' %(installdir)s/*.pl",
-    "chmod +x %(installdir)s/*.pl",
-]
+# this is the script which relies in many extra Perl libraries so we verify it's working fine
+sanity_check_commands = ['%(installdir)s/prinseq-graphs.pl']
 
 sanity_check_paths = {
     'files': ['prinseq-lite.pl', 'prinseq-graphs.pl', 'prinseq-graphs-noPCA.pl'],
     'dirs': []
 }
 
+modextrapaths = {
+    'PATH': '',
+    'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/',
+}
 
 moduleclass = 'bio'