satta

[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 ]

satta

### 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

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

#!/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)

satta

#!/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 = {}

satta

#!/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

satta

#!/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

# -*- 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.

satta

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

process test {
    output:
    file '*.out' into outfiles

    """
    touch "test'file.out"
    touch testfile2.out
    """
}