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@satta
satta / testout-ppc.txt
Created May 19, 2014
Failing tests on Linux/PPC
View testout-ppc.txt
[satta@renard:~] ◇ grep -A2 failed testout-ppc.txt
90: gt hcr reads : failed
[ problem: unexpected return code: 2 != 0
in: /root/genometools/testsuite/stest_testsuite/test90 ]
91: gt hcr reads allfiles : failed
[ problem: unexpected return code: 2 != 0
in: /root/genometools/testsuite/stest_testsuite/test91 ]
92: gt hcr reads and description : failed
[ problem: unexpected return code: 2 != 0
in: /root/genometools/testsuite/stest_testsuite/test92 ]
View gist:c45dddaf988914c39d69
### Keybase proof
I hereby claim:
* I am satta on github.
* I am satta (https://keybase.io/satta) on keybase.
* I have a public key whose fingerprint is 0EED 77DC 41D7 60FD E440 35FF 5556 A34E 04A3 610B
To claim this, I am signing this object:
@satta
satta / gist:e6a6c179dac88fcbd51f
Created Sep 5, 2014
simple gene extractor for access time testing
View gist:e6a6c179dac88fcbd51f
rm = gt.region_mapping_new_seqfile_matchdescstart(arg[2])
cv = gt.custom_visitor_new()
function cv:visit_feature(fn)
if fn:get_type() == "gene" then
print(fn:extract_sequence("gene", false, rm):len())
end
end
gs = gt.gff3_in_stream_new_sorted(arg[1])
@satta
satta / gff3_to_json.lua
Last active Aug 29, 2015
GFF3 to JSON converter
View gff3_to_json.lua
#!/usr/bin/env gt
function usage()
io.stderr:write(string.format("Usage: %s <GFF file>\n" , arg[0]))
os.exit(1)
end
if #arg < 1 then
usage()
os.exit(1)
View gist:51f1427d54cc42ec969a
#!/usr/bin/env ruby
if ARGV.length != 2 then
STDERR.puts "Usage: #{$0} <pfamfile> <directory>"
exit 1
end
file = File.open(ARGV[0]).read
seen_accs = {}
View add_mrna.lua
#!/usr/bin/env gt
function usage()
io.stderr:write(string.format("Usage: %s <GFF annotation>\n" , arg[0]))
os.exit(1)
end
if #arg < 1 then
usage()
end
View bequeath.lua
#!/usr/bin/env gt
function usage()
io.stderr:write("Adds a given parent attribute to all child features.\n")
io.stderr:write(string.format("Usage: %s <attribute> < <GFF>\n" , arg[0]))
os.exit(1)
end
if #arg < 1 then
usage()
@satta
satta / Vagrantfile
Last active Dec 15, 2015
Vagrantfile for AEGeAn debugging
View Vagrantfile
# -*- mode: ruby -*-
# vi: set ft=ruby :
VAGRANTFILE_API_VERSION = "2"
Vagrant.configure(VAGRANTFILE_API_VERSION) do |config|
config.vm.box = "debian/jessie64"
config.vm.box_check_update = false
config.vbguest.auto_update = false
# Create a public network, which generally matched to bridged network.
View nextflow.log
Oct-10 09:48:10.629 [main] DEBUG nextflow.cli.Launcher - Setting http proxy: [wwwcache.sanger.ac.uk, 3128]
Oct-10 09:48:10.759 [main] DEBUG nextflow.cli.Launcher - Setting https proxy: [wwwcache.sanger.ac.uk, 3128]
Oct-10 09:48:10.760 [main] DEBUG nextflow.cli.Launcher - $> /nfs/users/nfs_s/ss34//nextflow -c /nfs/users/nfs_s/ss34/annot-nf/loc_we
b.config -c /www/ss34/annot-web/public/jobs/cb1584075907314fa80d0419/config run /nfs/users/nfs_s/ss34/annot-nf/annot.nf -resume --di
st_dir /www/ss34/annot-web/public/jobs/cb1584075907314fa80d0419
Oct-10 09:48:10.760 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 0.15.3
Oct-10 09:48:10.760 [main] INFO nextflow.cli.CmdRun - Launching /nfs/users/nfs_s/ss34/annot-nf/annot.nf
Oct-10 09:48:10.780 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /nfs/users/nfs_s/ss34/annot-nf/nextflow.config
Oct-10 09:48:10.783 [main] DEBUG nextflow.config.ConfigBuilder - User config file: /nfs/users/nfs_s/ss34/annot-nf/loc_web.config
Oct-10 09:48:10.783 [mai
@satta
satta / test.nf
Created Jan 6, 2016
Test workflow for single quote problem
View test.nf
process test {
output:
file '*.out' into outfiles
"""
touch "test'file.out"
touch testfile2.out
"""
}
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