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@nathanhaigh
nathanhaigh / trackList.json
Last active Jul 4, 2018
Callbacks to generate links for Dbxref and Ontology_term entries in JBrowse GFF tracks
View trackList.json
"fmtDetailValue_Dbxref" : "function(dbxref){if(typeof dbxref!='string'){return dbxref}var dbid=dbxref.split(':');var prefix='';switch(dbid[0].toLowerCase()){case 'interpro':prefix='http://www.ebi.ac.uk/interpro/entry/';break;case 'pfam':prefix='http://pfam.sanger.ac.uk/family/';break;case 'reactome':prefix='http://www.reactome.org/content/detail/';break;case 'unipathway':prefix='http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upa?upid=';break;case 'kegg':prefix='http://www.genome.jp/kegg-bin/show_pathway?ec';break;case 'prositepatterns':prefix='http://prosite.expasy.org/';break;case 'prositeprofiles':prefix='http://prosite.expasy.org/cgi-bin/prosite/PSView.cgi?ac=';break;case 'smart':prefix='http://smart.embl-heidelberg.de/smart/do_annotation.pl?BLAST=DUMMY&DOMAIN=';break;case 'superfamily':prefix='http://supfam.org/SUPERFAMILY/cgi-bin/scop.cgi?sunid=';dbid[1]=dbid[1].replace('SSF','');break;case 'gene3d':prefix='http://www.cathdb.info/version/latest/superfamily/';dbid[1]=dbid[2];break;case 'pirsf':prefi
@nathanhaigh
nathanhaigh / gff3_split.pl
Last active Jun 8, 2017
Perl script to perform coordinate transformation on GFF3 files when reference sequences are split into multiple pieces.
View gff3_split.pl
#!/usr/bin/env perl
use strict;
use warnings;
my $bed_file = shift @ARGV;
my $suffix_fmt = '_part%01d';
open(my $bed_fh, '<', $bed_file) || die "Couldn't open BED file: $!\n";
my %cut_positions;
@nathanhaigh
nathanhaigh / depth2bedgraph.awk
Created Jun 7, 2017
Converts the output of samtools depth into bedgraph format
View depth2bedgraph.awk
#!/usr/bin/awk
# Takes output of "samtools depth" and reformats into grouped bedgraph format:
# samtools depth -r ${loc} -Q 1 --reference $fasta $bam | mawk -f scripts/depth2bedgraph.awk > /tmp/my.bedgraph
# Example input:
#chr1 26 2
#chr1 27 2
#chr1 28 2
#chr1 29 5
#chr1 30 5
#chr1 31 5
View easybuild_test_report_easyconfigs_pr2314_20164012-UTC-06-40-19.md

Test report for https://github.com/hpcugent/easybuild-easyconfigs/pull/2314

Test result

Build succeeded for 31 out of 32 (32 easyconfigs in this PR)

Overview of tested easyconfigs (in order)

  • SUCCESS xcb-proto-1.11-foss-2015b-Python-2.7.10.eb
  • SUCCESS kbproto-1.0.7-foss-2015b.eb
  • SUCCESS expat-2.1.0-foss-2015b.eb
  • SUCCESS renderproto-0.11-foss-2015b.eb
@nathanhaigh
nathanhaigh / cairo-1.14.6-foss-2015b_partial.log
Created Jan 12, 2016
(partial) EasyBuild log for failed build of /tmp/eb-lb1o5q/files_pr2314/cairo-1.14.6-foss-2015b.eb (PR #2314)
View cairo-1.14.6-foss-2015b_partial.log
== 2016-01-12 16:52:01,574 runpy.run DEBUG run_cmd: running cmd make -j 10 (in /mnt/bioinf-7/easybuild/build/cairo/1.14.6/foss-2015b/cairo-1.14.6)
== 2016-01-12 16:52:15,094 runpy.run DEBUG cmd " make -j 10 " exited with exitcode 2 and output:
Makefile:1487: warning: overriding commands for target `recheck'
Makefile:1127: warning: ignoring old commands for target `recheck'
make all-recursive
make[1]: Entering directory `/mnt/bioinf-7/easybuild/build/cairo/1.14.6/foss-2015b/cairo-1.14.6'
Makefile:1487: warning: overriding commands for target `recheck'
Makefile:1127: warning: ignoring old commands for target `recheck'
Making all in src
make[2]: Entering directory `/mnt/bioinf-7/easybuild/build/cairo/1.14.6/foss-2015b/cairo-1.14.6/src'
View easybuild_test_report_easyconfigs_pr2096_20160512-UTC-01-05-42.md

Test report for https://github.com/hpcugent/easybuild-easyconfigs/pull/2096

Test result

Build succeeded for 13 out of 24 (11 easyconfigs in this PR)

Overview of tested easyconfigs (in order)

  • SUCCESS Autoconf-2.69.eb
  • SUCCESS libtool-2.4.6.eb
  • SUCCESS Automake-1.15.eb
  • SUCCESS Autotools-20150215.eb
@nathanhaigh
nathanhaigh / GMP-6.0.0a-intel-2015b_partial.log
Created Jan 12, 2016
(partial) EasyBuild log for failed build of /tmp/eb-_EnA1J/files_pr2096/GMP-6.0.0a-intel-2015b.eb (PR #2096)
View GMP-6.0.0a-intel-2015b_partial.log
GNU/4.9.3-2.25
foss/
foss/2015a
foss/2015b
gompi/
gompi/1.5.16
gompi/1.7.20
gompi/2.1.10
gompi/2015a
gompi/2015b
@nathanhaigh
nathanhaigh / intel-2015b_partial.log
Created Jan 12, 2016
(partial) EasyBuild log for failed build of /home/bioadmin/git_repos/easybuild-easyconfigs/easybuild/easyconfigs/i/intel/intel-2015b.eb (PR #2096)
View intel-2015b_partial.log
== 2016-01-12 11:35:08,265 runpy.Toolchain INFO This is EasyBuild 2.5.0 (framework: 2.5.0, easyblocks: 2.5.0) on host acpfg-bioserv2.
== 2016-01-12 11:35:08,266 runpy.Toolchain INFO This is easyblock Toolchain from module easybuild.easyblocks.generic.toolchain (/opt/shared_apps/easybuild/software/EasyBuild/2.5.0/lib/python2.7/site-packages/easybuild_easyblocks-2.5.0-py2.7.egg/easybuild/easyblocks/generic/toolchain.pyc)
== 2016-01-12 11:35:08,266 runpy.Toolchain INFO Build dir set to /opt/shared_apps/easybuild/build/intel/2015b/dummy-dummy
== 2016-01-12 11:35:08,266 runpy.config DEBUG software install path as specified by 'installpath' and 'subdir_software': /opt/shared_apps/easybuild/software
== 2016-01-12 11:35:08,267 runpy.ActiveMNS DEBUG Determining software installation subdir for <easybuild.framework.easyconfig.easyconfig.EasyConfig object at 0x7f09f17084d0>
== 2016-01-12 11:35:08,267 runpy.ActiveMNS DEBUG Obtained subdir intel/2015b
== 2016-01-12 11:35:08,267 runpy.Toolchain INFO Software install dir se
@nathanhaigh
nathanhaigh / imkl-11.2.3.187-iimpi-7.3.5-GNU-4.9.3-2.25_partial.log
Created Jan 12, 2016
(partial) EasyBuild log for failed build of /home/bioadmin/git_repos/easybuild-easyconfigs/easybuild/easyconfigs/i/imkl/imkl-11.2.3.187-iimpi-7.3.5-GNU-4.9.3-2.25.eb (PR #2096)
View imkl-11.2.3.187-iimpi-7.3.5-GNU-4.9.3-2.25_partial.log
== 2016-01-12 11:35:06,604 runpy.EB_imkl INFO This is EasyBuild 2.5.0 (framework: 2.5.0, easyblocks: 2.5.0) on host acpfg-bioserv2.
== 2016-01-12 11:35:06,604 runpy.EB_imkl INFO This is easyblock EB_imkl from module easybuild.easyblocks.imkl (/opt/shared_apps/easybuild/software/EasyBuild/2.5.0/lib/python2.7/site-packages/easybuild_easyblocks-2.5.0-py2.7.egg/easybuild/easyblocks/i/imkl.pyc)
== 2016-01-12 11:35:06,605 runpy.EB_imkl INFO Build dir set to /opt/shared_apps/easybuild/build/imkl/11.2.3.187/iimpi-7.3.5-GNU-4.9.3-2.25
== 2016-01-12 11:35:06,605 runpy.config DEBUG software install path as specified by 'installpath' and 'subdir_software': /opt/shared_apps/easybuild/software
== 2016-01-12 11:35:06,605 runpy.ActiveMNS DEBUG Determining software installation subdir for <easybuild.framework.easyconfig.easyconfig.EasyConfig object at 0x7f09f16f94d0>
== 2016-01-12 11:35:06,606 runpy.ActiveMNS DEBUG Obtained subdir imkl/11.2.3.187-iimpi-7.3.5-GNU-4.9.3-2.25
== 2016-01-12 11:35:06,606 runpy.EB_imkl INFO Softwar
@nathanhaigh
nathanhaigh / iimpi-7.3.5-GNU-4.9.3-2.25_partial.log
Created Jan 12, 2016
(partial) EasyBuild log for failed build of /home/bioadmin/git_repos/easybuild-easyconfigs/easybuild/easyconfigs/i/iimpi/iimpi-7.3.5-GNU-4.9.3-2.25.eb (PR #2096)
View iimpi-7.3.5-GNU-4.9.3-2.25_partial.log
== 2016-01-12 11:35:04,415 runpy.Toolchain INFO This is EasyBuild 2.5.0 (framework: 2.5.0, easyblocks: 2.5.0) on host acpfg-bioserv2.
== 2016-01-12 11:35:04,415 runpy.Toolchain INFO This is easyblock Toolchain from module easybuild.easyblocks.generic.toolchain (/opt/shared_apps/easybuild/software/EasyBuild/2.5.0/lib/python2.7/site-packages/easybuild_easyblocks-2.5.0-py2.7.egg/easybuild/easyblocks/generic/toolchain.pyc)
== 2016-01-12 11:35:04,416 runpy.Toolchain INFO Build dir set to /opt/shared_apps/easybuild/build/iimpi/7.3.5/dummy-dummy-GNU-4.9.3-2.25
== 2016-01-12 11:35:04,416 runpy.config DEBUG software install path as specified by 'installpath' and 'subdir_software': /opt/shared_apps/easybuild/software
== 2016-01-12 11:35:04,416 runpy.ActiveMNS DEBUG Determining software installation subdir for <easybuild.framework.easyconfig.easyconfig.EasyConfig object at 0x7f09f16a2650>
== 2016-01-12 11:35:04,416 runpy.ActiveMNS DEBUG Obtained subdir iimpi/7.3.5-GNU-4.9.3-2.25
== 2016-01-12 11:35:04,417 runpy.Toolchai
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