andrewcstewart

$ vagrant up
There were warnings and/or errors while loading your Vagrantfile.
Your Vagrantfile was written for an earlier version of Vagrant,
and while Vagrant does the best it can to remain backwards
compatible, there are some cases where things have changed
significantly enough to warrant a message. These messages are
shown below.

Warnings:
* `config.vm.customize` calls are VirtualBox-specific. If you're

andrewcstewart

import B as b

b.D()

andrewcstewart

/bin/sh: raxmlHPC-PTHREADS-SSE3: command not found
Return error code 127 from command:
['raxmlHPC-PTHREADS-SSE3', '-T 4', '-s /home/galaxy/galaxy-dist/database/files/000/dataset_76.dat', '-n galaxy', '-m GTRGAMMA', '-p 1234567890']

andrewcstewart

#!/usr/bin/perl -w
for ($job in @ARGV) {
  system "qsub $job";
}

andrewcstewart

# -*- mode: ruby -*-
# vi: set ft=ruby :
require 'yaml'

Vagrant.configure("2") do |config|
  # All Vagrant configuration is done here. The most common configuration
  # options are documented and commented below. For a complete reference,
  # please see the online documentation at vagrantup.com.

  # Every Vagrant virtual environment requires a box to build off of.

andrewcstewart

In [26]: pid = client.getNextPID(u'foo')
---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
<ipython-input-26-9c5d45fed03c> in <module>()
----> 1 pid = client.getNextPID(u'foo')

/Library/Python/2.7/site-packages/fcrepo/client.pyc in getNextPID(self, namespace, numPIDs, format)
     19
     20     def getNextPID(self, namespace, numPIDs=1, format=u'text/xml'):
---> 21         request = self.api.getNextPID()

andrewcstewart

#!/usr/bin/perl -w

while(<>) {
  chomp($_);
  my @o = split("",$_);
  print join(',',@o) . "\n";
}

andrewcstewart

import sys
from Bio import SearchIO

# usage: parse_blast_hits.py inputfile > outputfile

file = sys.argv[1]

for qresult in SearchIO.parse(file, 'blast-text'):
  print("%s" % (qresult.id))

andrewcstewart

# Paste URLs and other text here for easier copying

http://cloud1.galaxyproject.org/

andrewcstewart

FROM centos

RUN yum install -y tar wget postgresql-devel
RUN wget http://bin.begriffs.com/dbapi/heroku/postgrest-0.2.8.0.tar.xz
RUN tar --xz -xvf postgrest-0.2.8.0.tar.xz
RUN mv postgrest-0.2.8.0 /usr/local/bin/postgrest

CMD postgrest  --db-host localhost  --db-port 5432     \
               --db-name my_db      --db-user postgres \
               --db-pass foobar     --db-pool 200      \