From f91b3b8c30dab7ae7b30a4254dd3c28d6db4231d Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Mon, 16 Dec 2024 12:52:14 +0100 Subject: [PATCH] #467 annovar + working pre-PR version --- 467_scNanoGPS/annovar.eb | 9 ++------- 467_scNanoGPS/scNanoGPS_v2.eb | 12 +++++++++--- 2 files changed, 11 insertions(+), 10 deletions(-) diff --git a/467_scNanoGPS/annovar.eb b/467_scNanoGPS/annovar.eb index 724d59d4..19fd3f0a 100644 --- 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 index e8d16719..72daf9db 100644 --- 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'