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Repository 'cdhit'
http://toolshed.g2.bx.psu.edu/view/jjohnson/cdhit
hg clone http://toolshed.g2.bx.psu.edu/repos/jjohnson/cdhit
cdhit
unrestricted
cd-hit - reduce a collection of sequences to a representative sample
Cluster a set of sequences to generate a set of representative sequences.  http://weizhong-lab.ucsd.edu/cd-hit/wiki/doku.php?id=cd-hit_user_guide
3:43724ea1c85f
jjohnson
True
325

Repository README files - may contain important installation or license information

CD-HIT-EST

CD-HIT-EST clusters a nucleotide dataset into clusters that meet a user-defined similarity threshold, usually a sequence identity. The input is a DNA/RNA dataset in fasta format and the output are two files: a fasta file of representative sequences and a text file of list of clusters. Since eukaryotic genes usually have long introns, which cause long gaps, it is difficult to make full-length alignments for these genes. So, CD-HIT-EST is good for non-intron containing sequences like EST.

Ying Huang, Beifang Niu, Ying Gao, Limin Fu and Weizhong Li. CD-HIT Suite: a web server for clustering and comparing biological sequences. Bioinformatics, (2010). 26:680


From: http://weizhong-lab.ucsd.edu/cd-hit/wiki/doku.php?id=cd-hit_user_guide


CD-HIT was originally a protein clustering program. The main advantage of this program is its ultra-fast speed. It can be hundreds of times faster than other clustering programs, for example, BLASTCLUST. Therefore it can handle very large databases, like NR.

The 1st version of this program, CD-HI, was published and released in 2001. The 2nd version, called CD-HIT, was published in 2002 with significant improvements. Since 2004, CD-HIT has been hosted at bioinformatics.org as an open source project.

Since its release, CD-HIT has been getting more and more popular. It has a significant user base, I estimated at over several thousands users. It is used at many research and educational institutions. For example, at UniProt, CD-HIT is used to generate the UniRef reference data sets (http://www.pir.uniprot.org/database/DBDescription.shtml). It is also used in PDB to treat redundant sequences (http://rutgers.rcsb.org/pdb/redundancy.html).

In 2006, the 3rd major updates were published and released with abilities to perform various jobs like clustering a protein database, clustering a DNA/RNA database, comparing two databases (protein or DNA/RNA), generating protein families, and many others.

The CD-HIT web server was implemented in 2009, which allows users to cluster or compare sequences without using command CD-HIT. The server provides interactive interface and additional visualization tools. It also provides pre-calculated and regularly updated sequence clusters for several widely used databases.

CD-HIT-454, a special version of CD-HIT was implemented in 2010 to cluster artificial duplicated reads in pyrosequencing (454) data.

Currently, CD-HIT package has many programs: cd-hit, cd-hit-2d, cd-hit-est, cd-hit-est-2d, cd-hit-para, cd-hit-2d-para, psi-cd-hit, psi-cd-hit-2d, cd-hit-454. I also developed some utility tools, written in Perl, to help run and analyze CD-HIT jobs.


NOTE to installer:   
The tool_dependency will set an environment variable: "CDHIT_SITE_OPTIONS" to -M 4000 -T 0  which will be in the commandline.  
You can adjust the values of -M and -T to match the memory and thread capabilities of your site.

Dependencies of this repository

Name Version Type
cd-hit 4.6.1 package

Contents of this repository

Name Description Version
CD-HIT PROTEIN Cluster a protein dataset into representative sequences 1.2
CD-HIT-EST Cluster a nucleotide dataset into representative sequences 1.2

Automated tool test results

Time tested: 2014-04-17 05:38:11
System: Linux 3.8.0-30-generic
Architecture: x86_64
Python version: 2.7.4
Galaxy revision: 13085:c05752549163
Galaxy database version: 118
Tool shed revision: 12961:888478c66456
Tool shed database version: 22
Tool shed mercurial version: 2.2.3
Tool id: cd_hit_est
Tool version: cd_hit_est
Test: test_tool_000000 (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/jjohnson/cdhit/cd_hit_est/1.2)
Stderr:
/bin/sh: 1: cd-hit-est: not found
Traceback:
Traceback (most recent call last):
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/functional/test_toolbox.py", line 106, in test_tool
    self.do_it( td )
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/functional/test_toolbox.py", line 34, in do_it
    self._verify_outputs( testdef, test_history, shed_tool_id, data_list, galaxy_interactor )
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/functional/test_toolbox.py", line 67, in _verify_outputs
    galaxy_interactor.verify_output( history, output_data, outfile, attributes=attributes, shed_tool_id=shed_tool_id, maxseconds=maxseconds )
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/base/interactor.py", line 321, in verify_output
    self.twill_test_case.verify_dataset_correctness( outfile, hid=hid, attributes=attributes, shed_tool_id=shed_tool_id, maxseconds=maxseconds )
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/base/twilltestcase.py", line 827, in verify_dataset_correctness
    self._assert_dataset_state( elem, 'ok' )
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/base/twilltestcase.py", line 641, in _assert_dataset_state
    raise AssertionError( errmsg )
AssertionError: Expecting dataset state 'ok', but state is 'error'. Dataset blurb: error
Tool id: cd_hit_est
Tool version: cd_hit_est
Test: test_tool_000001 (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/jjohnson/cdhit/cd_hit_est/1.2)
Stderr:
/bin/sh: 1: cd-hit-est: not found
Traceback:
Traceback (most recent call last):
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/functional/test_toolbox.py", line 106, in test_tool
    self.do_it( td )
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/functional/test_toolbox.py", line 34, in do_it
    self._verify_outputs( testdef, test_history, shed_tool_id, data_list, galaxy_interactor )
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/functional/test_toolbox.py", line 67, in _verify_outputs
    galaxy_interactor.verify_output( history, output_data, outfile, attributes=attributes, shed_tool_id=shed_tool_id, maxseconds=maxseconds )
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/base/interactor.py", line 321, in verify_output
    self.twill_test_case.verify_dataset_correctness( outfile, hid=hid, attributes=attributes, shed_tool_id=shed_tool_id, maxseconds=maxseconds )
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/base/twilltestcase.py", line 827, in verify_dataset_correctness
    self._assert_dataset_state( elem, 'ok' )
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/base/twilltestcase.py", line 641, in _assert_dataset_state
    raise AssertionError( errmsg )
AssertionError: Expecting dataset state 'ok', but state is 'error'. Dataset blurb: error
Tool id: cd_hit_protein
Tool version: cd_hit_protein
Test: test_tool_000000 (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/jjohnson/cdhit/cd_hit_protein/1.2)
Stderr:
/bin/sh: 1: cd-hit: not found
Traceback:
Traceback (most recent call last):
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/functional/test_toolbox.py", line 106, in test_tool
    self.do_it( td )
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/functional/test_toolbox.py", line 34, in do_it
    self._verify_outputs( testdef, test_history, shed_tool_id, data_list, galaxy_interactor )
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/functional/test_toolbox.py", line 67, in _verify_outputs
    galaxy_interactor.verify_output( history, output_data, outfile, attributes=attributes, shed_tool_id=shed_tool_id, maxseconds=maxseconds )
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/base/interactor.py", line 321, in verify_output
    self.twill_test_case.verify_dataset_correctness( outfile, hid=hid, attributes=attributes, shed_tool_id=shed_tool_id, maxseconds=maxseconds )
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/base/twilltestcase.py", line 827, in verify_dataset_correctness
    self._assert_dataset_state( elem, 'ok' )
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/base/twilltestcase.py", line 641, in _assert_dataset_state
    raise AssertionError( errmsg )
AssertionError: Expecting dataset state 'ok', but state is 'error'. Dataset blurb: error
Tool id: cd_hit_protein
Tool version: cd_hit_protein
Test: test_tool_000001 (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/jjohnson/cdhit/cd_hit_protein/1.2)
Stderr:
/bin/sh: 1: cd-hit: not found
Traceback:
Traceback (most recent call last):
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/functional/test_toolbox.py", line 106, in test_tool
    self.do_it( td )
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/functional/test_toolbox.py", line 34, in do_it
    self._verify_outputs( testdef, test_history, shed_tool_id, data_list, galaxy_interactor )
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/functional/test_toolbox.py", line 67, in _verify_outputs
    galaxy_interactor.verify_output( history, output_data, outfile, attributes=attributes, shed_tool_id=shed_tool_id, maxseconds=maxseconds )
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/base/interactor.py", line 321, in verify_output
    self.twill_test_case.verify_dataset_correctness( outfile, hid=hid, attributes=attributes, shed_tool_id=shed_tool_id, maxseconds=maxseconds )
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/base/twilltestcase.py", line 827, in verify_dataset_correctness
    self._assert_dataset_state( elem, 'ok' )
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/base/twilltestcase.py", line 641, in _assert_dataset_state
    raise AssertionError( errmsg )
AssertionError: Expecting dataset state 'ok', but state is 'error'. Dataset blurb: error
TypeNameVersion
cd-hit package 4.6.1
Installation directory
/ToolDepsMain/cd-hit/4.6.1/jjohnson/cdhit/43724ea1c85f
Time tested: 2014-04-16 05:32:32
System: Linux 3.8.0-30-generic
Architecture: x86_64
Python version: 2.7.4
Galaxy revision: 13065:1ad62c772728
Galaxy database version: 118
Tool shed revision: 12961:888478c66456
Tool shed database version: 22
Tool shed mercurial version: 2.2.3
Tool id: cd_hit_est
Tool version: cd_hit_est
Test: test_tool_000000 (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/jjohnson/cdhit/cd_hit_est/1.2)
Stderr:
/bin/sh: 1: cd-hit-est: not found
Traceback:
Traceback (most recent call last):
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/functional/test_toolbox.py", line 106, in test_tool
    self.do_it( td )
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/functional/test_toolbox.py", line 34, in do_it
    self._verify_outputs( testdef, test_history, shed_tool_id, data_list, galaxy_interactor )
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/functional/test_toolbox.py", line 67, in _verify_outputs
    galaxy_interactor.verify_output( history, output_data, outfile, attributes=attributes, shed_tool_id=shed_tool_id, maxseconds=maxseconds )
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/base/interactor.py", line 321, in verify_output
    self.twill_test_case.verify_dataset_correctness( outfile, hid=hid, attributes=attributes, shed_tool_id=shed_tool_id, maxseconds=maxseconds )
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/base/twilltestcase.py", line 827, in verify_dataset_correctness
    self._assert_dataset_state( elem, 'ok' )
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/base/twilltestcase.py", line 641, in _assert_dataset_state
    raise AssertionError( errmsg )
AssertionError: Expecting dataset state 'ok', but state is 'error'. Dataset blurb: error
Tool id: cd_hit_est
Tool version: cd_hit_est
Test: test_tool_000001 (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/jjohnson/cdhit/cd_hit_est/1.2)
Stderr:
/bin/sh: 1: cd-hit-est: not found
Traceback:
Traceback (most recent call last):
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/functional/test_toolbox.py", line 106, in test_tool
    self.do_it( td )
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/functional/test_toolbox.py", line 34, in do_it
    self._verify_outputs( testdef, test_history, shed_tool_id, data_list, galaxy_interactor )
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/functional/test_toolbox.py", line 67, in _verify_outputs
    galaxy_interactor.verify_output( history, output_data, outfile, attributes=attributes, shed_tool_id=shed_tool_id, maxseconds=maxseconds )
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/base/interactor.py", line 321, in verify_output
    self.twill_test_case.verify_dataset_correctness( outfile, hid=hid, attributes=attributes, shed_tool_id=shed_tool_id, maxseconds=maxseconds )
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/base/twilltestcase.py", line 827, in verify_dataset_correctness
    self._assert_dataset_state( elem, 'ok' )
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/base/twilltestcase.py", line 641, in _assert_dataset_state
    raise AssertionError( errmsg )
AssertionError: Expecting dataset state 'ok', but state is 'error'. Dataset blurb: error
Tool id: cd_hit_protein
Tool version: cd_hit_protein
Test: test_tool_000000 (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/jjohnson/cdhit/cd_hit_protein/1.2)
Stderr:
/bin/sh: 1: cd-hit: not found
Traceback:
Traceback (most recent call last):
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/functional/test_toolbox.py", line 106, in test_tool
    self.do_it( td )
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/functional/test_toolbox.py", line 34, in do_it
    self._verify_outputs( testdef, test_history, shed_tool_id, data_list, galaxy_interactor )
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/functional/test_toolbox.py", line 67, in _verify_outputs
    galaxy_interactor.verify_output( history, output_data, outfile, attributes=attributes, shed_tool_id=shed_tool_id, maxseconds=maxseconds )
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/base/interactor.py", line 321, in verify_output
    self.twill_test_case.verify_dataset_correctness( outfile, hid=hid, attributes=attributes, shed_tool_id=shed_tool_id, maxseconds=maxseconds )
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/base/twilltestcase.py", line 827, in verify_dataset_correctness
    self._assert_dataset_state( elem, 'ok' )
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/base/twilltestcase.py", line 641, in _assert_dataset_state
    raise AssertionError( errmsg )
AssertionError: Expecting dataset state 'ok', but state is 'error'. Dataset blurb: error
Tool id: cd_hit_protein
Tool version: cd_hit_protein
Test: test_tool_000001 (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/jjohnson/cdhit/cd_hit_protein/1.2)
Stderr:
/bin/sh: 1: cd-hit: not found
Traceback:
Traceback (most recent call last):
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/functional/test_toolbox.py", line 106, in test_tool
    self.do_it( td )
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/functional/test_toolbox.py", line 34, in do_it
    self._verify_outputs( testdef, test_history, shed_tool_id, data_list, galaxy_interactor )
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/functional/test_toolbox.py", line 67, in _verify_outputs
    galaxy_interactor.verify_output( history, output_data, outfile, attributes=attributes, shed_tool_id=shed_tool_id, maxseconds=maxseconds )
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/base/interactor.py", line 321, in verify_output
    self.twill_test_case.verify_dataset_correctness( outfile, hid=hid, attributes=attributes, shed_tool_id=shed_tool_id, maxseconds=maxseconds )
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/base/twilltestcase.py", line 827, in verify_dataset_correctness
    self._assert_dataset_state( elem, 'ok' )
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/base/twilltestcase.py", line 641, in _assert_dataset_state
    raise AssertionError( errmsg )
AssertionError: Expecting dataset state 'ok', but state is 'error'. Dataset blurb: error
TypeNameVersion
cd-hit package 4.6.1
Installation directory
/ToolDepsMain/cd-hit/4.6.1/jjohnson/cdhit/43724ea1c85f
Time tested: 2014-04-15 06:06:53
System: Linux 3.8.0-30-generic
Architecture: x86_64
Python version: 2.7.4
Galaxy revision: 13058:1165a5a1221a
Galaxy database version: 118
Tool shed revision: 12961:888478c66456
Tool shed database version: 22
Tool shed mercurial version: 2.2.3
Tool id: cd_hit_est
Tool version: cd_hit_est
Test: test_tool_000000 (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/jjohnson/cdhit/cd_hit_est/1.2)
Stderr:
/bin/sh: 1: cd-hit-est: not found
Traceback:
Traceback (most recent call last):
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/functional/test_toolbox.py", line 106, in test_tool
    self.do_it( td )
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/functional/test_toolbox.py", line 34, in do_it
    self._verify_outputs( testdef, test_history, shed_tool_id, data_list, galaxy_interactor )
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/functional/test_toolbox.py", line 67, in _verify_outputs
    galaxy_interactor.verify_output( history, output_data, outfile, attributes=attributes, shed_tool_id=shed_tool_id, maxseconds=maxseconds )
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/base/interactor.py", line 321, in verify_output
    self.twill_test_case.verify_dataset_correctness( outfile, hid=hid, attributes=attributes, shed_tool_id=shed_tool_id, maxseconds=maxseconds )
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/base/twilltestcase.py", line 827, in verify_dataset_correctness
    self._assert_dataset_state( elem, 'ok' )
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/base/twilltestcase.py", line 641, in _assert_dataset_state
    raise AssertionError( errmsg )
AssertionError: Expecting dataset state 'ok', but state is 'error'. Dataset blurb: error
Tool id: cd_hit_est
Tool version: cd_hit_est
Test: test_tool_000001 (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/jjohnson/cdhit/cd_hit_est/1.2)
Stderr:
/bin/sh: 1: cd-hit-est: not found
Traceback:
Traceback (most recent call last):
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/functional/test_toolbox.py", line 106, in test_tool
    self.do_it( td )
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/functional/test_toolbox.py", line 34, in do_it
    self._verify_outputs( testdef, test_history, shed_tool_id, data_list, galaxy_interactor )
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/functional/test_toolbox.py", line 67, in _verify_outputs
    galaxy_interactor.verify_output( history, output_data, outfile, attributes=attributes, shed_tool_id=shed_tool_id, maxseconds=maxseconds )
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/base/interactor.py", line 321, in verify_output
    self.twill_test_case.verify_dataset_correctness( outfile, hid=hid, attributes=attributes, shed_tool_id=shed_tool_id, maxseconds=maxseconds )
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/base/twilltestcase.py", line 827, in verify_dataset_correctness
    self._assert_dataset_state( elem, 'ok' )
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/base/twilltestcase.py", line 641, in _assert_dataset_state
    raise AssertionError( errmsg )
AssertionError: Expecting dataset state 'ok', but state is 'error'. Dataset blurb: error
Tool id: cd_hit_protein
Tool version: cd_hit_protein
Test: test_tool_000000 (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/jjohnson/cdhit/cd_hit_protein/1.2)
Stderr:
/bin/sh: 1: cd-hit: not found
Traceback:
Traceback (most recent call last):
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/functional/test_toolbox.py", line 106, in test_tool
    self.do_it( td )
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/functional/test_toolbox.py", line 34, in do_it
    self._verify_outputs( testdef, test_history, shed_tool_id, data_list, galaxy_interactor )
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/functional/test_toolbox.py", line 67, in _verify_outputs
    galaxy_interactor.verify_output( history, output_data, outfile, attributes=attributes, shed_tool_id=shed_tool_id, maxseconds=maxseconds )
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/base/interactor.py", line 321, in verify_output
    self.twill_test_case.verify_dataset_correctness( outfile, hid=hid, attributes=attributes, shed_tool_id=shed_tool_id, maxseconds=maxseconds )
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/base/twilltestcase.py", line 827, in verify_dataset_correctness
    self._assert_dataset_state( elem, 'ok' )
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/base/twilltestcase.py", line 641, in _assert_dataset_state
    raise AssertionError( errmsg )
AssertionError: Expecting dataset state 'ok', but state is 'error'. Dataset blurb: error
Tool id: cd_hit_protein
Tool version: cd_hit_protein
Test: test_tool_000001 (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/jjohnson/cdhit/cd_hit_protein/1.2)
Stderr:
/bin/sh: 1: cd-hit: not found
Traceback:
Traceback (most recent call last):
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/functional/test_toolbox.py", line 106, in test_tool
    self.do_it( td )
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/functional/test_toolbox.py", line 34, in do_it
    self._verify_outputs( testdef, test_history, shed_tool_id, data_list, galaxy_interactor )
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/functional/test_toolbox.py", line 67, in _verify_outputs
    galaxy_interactor.verify_output( history, output_data, outfile, attributes=attributes, shed_tool_id=shed_tool_id, maxseconds=maxseconds )
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/base/interactor.py", line 321, in verify_output
    self.twill_test_case.verify_dataset_correctness( outfile, hid=hid, attributes=attributes, shed_tool_id=shed_tool_id, maxseconds=maxseconds )
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/base/twilltestcase.py", line 827, in verify_dataset_correctness
    self._assert_dataset_state( elem, 'ok' )
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/base/twilltestcase.py", line 641, in _assert_dataset_state
    raise AssertionError( errmsg )
AssertionError: Expecting dataset state 'ok', but state is 'error'. Dataset blurb: error
TypeNameVersion
cd-hit package 4.6.1
Installation directory
/ToolDepsMain/cd-hit/4.6.1/jjohnson/cdhit/43724ea1c85f
Time tested: 2014-04-14 05:29:30
System: Linux 3.8.0-30-generic
Architecture: x86_64
Python version: 2.7.4
Galaxy revision: 13041:b423b847f58e
Galaxy database version: 118
Tool shed revision: 12961:888478c66456
Tool shed database version: 22
Tool shed mercurial version: 2.2.3
Tool id: cd_hit_est
Tool version: cd_hit_est
Test: test_tool_000000 (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/jjohnson/cdhit/cd_hit_est/1.2)
Stderr:
/bin/sh: 1: cd-hit-est: not found
Traceback:
Traceback (most recent call last):
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/functional/test_toolbox.py", line 106, in test_tool
    self.do_it( td )
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/functional/test_toolbox.py", line 34, in do_it
    self._verify_outputs( testdef, test_history, shed_tool_id, data_list, galaxy_interactor )
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/functional/test_toolbox.py", line 67, in _verify_outputs
    galaxy_interactor.verify_output( history, output_data, outfile, attributes=attributes, shed_tool_id=shed_tool_id, maxseconds=maxseconds )
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/base/interactor.py", line 321, in verify_output
    self.twill_test_case.verify_dataset_correctness( outfile, hid=hid, attributes=attributes, shed_tool_id=shed_tool_id, maxseconds=maxseconds )
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/base/twilltestcase.py", line 827, in verify_dataset_correctness
    self._assert_dataset_state( elem, 'ok' )
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/base/twilltestcase.py", line 641, in _assert_dataset_state
    raise AssertionError( errmsg )
AssertionError: Expecting dataset state 'ok', but state is 'error'. Dataset blurb: error
Tool id: cd_hit_est
Tool version: cd_hit_est
Test: test_tool_000001 (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/jjohnson/cdhit/cd_hit_est/1.2)
Stderr:
/bin/sh: 1: cd-hit-est: not found
Traceback:
Traceback (most recent call last):
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/functional/test_toolbox.py", line 106, in test_tool
    self.do_it( td )
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/functional/test_toolbox.py", line 34, in do_it
    self._verify_outputs( testdef, test_history, shed_tool_id, data_list, galaxy_interactor )
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/functional/test_toolbox.py", line 67, in _verify_outputs
    galaxy_interactor.verify_output( history, output_data, outfile, attributes=attributes, shed_tool_id=shed_tool_id, maxseconds=maxseconds )
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/base/interactor.py", line 321, in verify_output
    self.twill_test_case.verify_dataset_correctness( outfile, hid=hid, attributes=attributes, shed_tool_id=shed_tool_id, maxseconds=maxseconds )
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/base/twilltestcase.py", line 827, in verify_dataset_correctness
    self._assert_dataset_state( elem, 'ok' )
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/base/twilltestcase.py", line 641, in _assert_dataset_state
    raise AssertionError( errmsg )
AssertionError: Expecting dataset state 'ok', but state is 'error'. Dataset blurb: error
Tool id: cd_hit_protein
Tool version: cd_hit_protein
Test: test_tool_000000 (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/jjohnson/cdhit/cd_hit_protein/1.2)
Stderr:
/bin/sh: 1: cd-hit: not found
Traceback:
Traceback (most recent call last):
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/functional/test_toolbox.py", line 106, in test_tool
    self.do_it( td )
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/functional/test_toolbox.py", line 34, in do_it
    self._verify_outputs( testdef, test_history, shed_tool_id, data_list, galaxy_interactor )
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/functional/test_toolbox.py", line 67, in _verify_outputs
    galaxy_interactor.verify_output( history, output_data, outfile, attributes=attributes, shed_tool_id=shed_tool_id, maxseconds=maxseconds )
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/base/interactor.py", line 321, in verify_output
    self.twill_test_case.verify_dataset_correctness( outfile, hid=hid, attributes=attributes, shed_tool_id=shed_tool_id, maxseconds=maxseconds )
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/base/twilltestcase.py", line 827, in verify_dataset_correctness
    self._assert_dataset_state( elem, 'ok' )
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/base/twilltestcase.py", line 641, in _assert_dataset_state
    raise AssertionError( errmsg )
AssertionError: Expecting dataset state 'ok', but state is 'error'. Dataset blurb: error
Tool id: cd_hit_protein
Tool version: cd_hit_protein
Test: test_tool_000001 (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/jjohnson/cdhit/cd_hit_protein/1.2)
Stderr:
/bin/sh: 1: cd-hit: not found
Traceback:
Traceback (most recent call last):
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/functional/test_toolbox.py", line 106, in test_tool
    self.do_it( td )
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/functional/test_toolbox.py", line 34, in do_it
    self._verify_outputs( testdef, test_history, shed_tool_id, data_list, galaxy_interactor )
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/functional/test_toolbox.py", line 67, in _verify_outputs
    galaxy_interactor.verify_output( history, output_data, outfile, attributes=attributes, shed_tool_id=shed_tool_id, maxseconds=maxseconds )
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/base/interactor.py", line 321, in verify_output
    self.twill_test_case.verify_dataset_correctness( outfile, hid=hid, attributes=attributes, shed_tool_id=shed_tool_id, maxseconds=maxseconds )
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/base/twilltestcase.py", line 827, in verify_dataset_correctness
    self._assert_dataset_state( elem, 'ok' )
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/base/twilltestcase.py", line 641, in _assert_dataset_state
    raise AssertionError( errmsg )
AssertionError: Expecting dataset state 'ok', but state is 'error'. Dataset blurb: error
TypeNameVersion
cd-hit package 4.6.1
Installation directory
/ToolDepsMain/cd-hit/4.6.1/jjohnson/cdhit/43724ea1c85f

Categories
Fasta Manipulation
Sequence Analysis