#467 annovar + working pre-PR version

vscentrum · Dec 16, 2024 · f91b3b8 · f91b3b8
1 parent fcd0590
commit f91b3b8
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Showing 2 changed files with 11 additions and 10 deletions.
diff --git a/467_scNanoGPS/annovar.eb b/467_scNanoGPS/annovar.eb
@@ -18,15 +18,10 @@ toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
 # rename after download to %(name)s-%(version)s.tar.gz
 sources = ['%(name)s-%(version)s.tar.gz']
 checksums = ['4061af3f2cc8f3d4d8187986c3d468a4b6ae145eec1858e85c7cd1059debb8ed']
-# www.openbioinformatics.org/annovar/download/0wgxr2rivp/annovar.latest.tar.gz
-# http://www.openbioinformatics.org/annovar/download/0wgxr2rivp/annovar.latest.tar.gz
-# http%3A%2F%2Fwww.openbioinformatics.org%2Fannovar%2Fdownload%2F0wgxR2rIVP%2Fannovar.latest.tar.gz
-# https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.openbioinformatics.org%2Fannovar%2Fdownload%2F0wgxR2rIVP%2Fannovar.latest.tar.gz&data=05%7C02%7CPavel.Tomanek%40ugent.be%7C2bc2be1ddbd04f55603d08dd1845a0f8%7Cd7811cdeecef496c8f91a1786241b99c%7C1%7C0%7C638693409652782873%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=Q7QUiPCDxkpeaXGu8wqgNC8kxmTVd8dWerNLHPVBc8I%3D&reserved=0
+
 dependencies = [('Perl', '5.36.1'),]
 
-modextrapaths = {
-    'PATH': '',
-}
+modextrapaths = {'PATH': ''}
 
 sanity_check_paths = {
     'files': ["annotate_variation.pl", "coding_change.pl", "convert2annovar.pl", "retrieve_seq_from_fasta.pl",

diff --git a/467_scNanoGPS/scNanoGPS_v2.eb b/467_scNanoGPS/scNanoGPS_v2.eb
@@ -32,7 +32,7 @@ checksums = ['60cce1c771283b6d7a3639aa5744acfd6162306d95dd419ad3c265461fdda218']
     # Optional:
         # OK gffread
         # Qualimap - not for 2023a 
-    # Liqa deps:
+    # Liqa deps: -> separate EC
         # OK Python
             # OK Pysam
             # OK Numpy
@@ -60,7 +60,7 @@ dependencies = [
     ('BCFtools', '1.21'),
     ('gffread', '0.12.7'),
     ('LIQA', '1.3.4'),
-    # annovar
+    # Optional - load 'annovar/20200607-GCCcore-12.3.0-Perl-5.36.1' to make reporter_SNV.py work
 ]
 
 exts_defaultclass = 'PythonPackage'
@@ -84,7 +84,6 @@ sanity_check_paths = {
 
 sanity_check_commands = [
     'liqa -h',
-    "python -c 'import distance'",
     "python other_utils/read_length_profiler.py -h",
     "python scanner.py -h",
     "python assigner.py -h",
@@ -97,4 +96,11 @@ sanity_check_commands = [
 
 modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'}
 
+modloadmsg = """
+If you like to use script 'reporter_SNV.py' you need to load annovar module as:
+'ml annovar/20200607-GCCcore-12.3.0-Perl-5.36.1'
+Source files of annovar (latest) are available after registration on:
+http://www.openbioinformatics.org/annovar/annovar_download_form.php
+"""
+
 moduleclass = 'bio'