Twill compares wrong file; was: Twill comparisons ignore GALAXY_TEST_NO_CLEANUP
by Peter Cock
On Tue, Feb 11, 2014 at 3:41 PM, Dave Bouvier <dave(a)bx.psu.edu> wrote:
> Peter,
>
> Thanks for pointing this out, I've applied your changes in
> 12478:15fc8675064e on the default branch.
>
> --Dave B.
Thanks Dave,
RE: http://lists.bx.psu.edu/pipermail/galaxy-dev/2014-February/018154.html
https://bitbucket.org/galaxy/galaxy-central/commits/15fc8675064ea46b7e081...
I'm still digging into the underlying problem, by focussing on just
one unit test from
https://github.com/peterjc/pico_galaxy/blob/master/tools/mira4/mira4_de_n...
Namely:
<test>
<param name="job_type" value="genome" />
<param name="job_quality" value="accurate" />
<param name="type" value="none" />
<param name="filenames" value="ecoli.fastq" ftype="fastqsanger" />
<output name="out_fasta" file="ecoli.mira4_de_novo.fasta"
ftype="fasta" />
</test>
After the test runs, we have five files, which is expected as I have
one input and four outputs:
<outputs>
<data name="out_fasta" format="fasta" label="MIRA de novo
contigs (FASTA)" />
<data name="out_bam" format="bam" label="MIRA de novo assembly (BAM)" />
<data name="out_maf" format="mira" label="MIRA de novo assembly" />
<data name="out_log" format="txt" label="MIRA de novo log" />
</outputs>
$ ls /tmp/tmp09TawY/tmpFOX9hS/database/files/000/
dataset_1.dat dataset_2.dat dataset_3.dat dataset_4.dat dataset_5.dat
dataset_1.dat --> test-data/ecoli.fastq
dataset_2.dat --> out_fasta
dataset_3.dat --> out_bam
dataset_4.dat --> out_maf
dataset_5.dat --> out_log
Of these, the test should only attempt to compare dataset_2.dat (out_fasta)
to my sample output file test-data/ecoli.mira4_de_novo.fasta which it matches:
$ diff test-data/ecoli.mira4_de_novo.fasta
/tmp/tmp09TawY/tmpFOX9hS/database/files/000/dataset_2.dat
However, for reasons unknown, it is comparing dataset_5.dat (out_log)
to the sample output file test-data/ecoli.mira4_de_novo.fasta instead.
A little more logging (e.g. [1]) shows the problem is when calling into the
verify_dataset_correctness method (should use hid=2):
base.interactor: DEBUG: About to call
verify_dataset_correctness('ecoli.mira4_de_novo.fasta', '5', ...)
base.interactor: DEBUG: About to call verify_dataset_correctness(...)
for output_data 'state': 'queued'
base.interactor: DEBUG: About to call verify_dataset_correctness(...)
for output_data 'hid': '5'
base.interactor: DEBUG: About to call verify_dataset_correctness(...)
for output_data 'id': '5'
base.interactor: DEBUG: About to call verify_dataset_correctness(...)
for output_data 'dbkey': 'hg17'
base.interactor: DEBUG: About to call verify_dataset_correctness(...)
for output_data 'name': 'MIRA de novo log'
base.twilltestcase: DEBUG: Verifying dataset correctness for
'ecoli.mira4_de_novo.fasta' (hid='5')
Now what is strange is how can the call to get the hid for the current
outfile can know if it should be 2, 3, 4, or 5? The bug appears to be
in method _verify_outputs in test/functional/test_toolbox.py - which
was last touched by John...
output_data = data_list[ len(data_list) - len(testdef.outputs) + output_index ]
In this example, we have data_list[5 - 1 + 0] = 4, meaning since
data_list is essentially [dataset_1, ..., dataset_5] we get dataset_5
I believe the error is that rather than the number of defined test outputs
(here 1), you should be subtracting the number of tool outputs (here 4).
i.e. data_list[5 - 4 + 0] = data_list[1] = dataset_2
As a workaround, I could probably provide expected data for all
four output files...
Regards,
Peter
[1] Patch which adds more logging to test/base/interactor.py
(similar debugging added to other files to trace this.)
$ hg diff test/base/interactor.py
diff -r f3dc213a5773 test/base/interactor.py
--- a/test/base/interactor.py Mon Feb 10 22:13:35 2014 -0600
+++ b/test/base/interactor.py Tue Feb 11 16:19:51 2014 +0000
@@ -309,6 +309,9 @@
def verify_output( self, history, output_data, outfile,
attributes, shed_tool_id, maxseconds ):
hid = output_data.get( 'hid' )
+ log.debug("About to call verify_dataset_correctness(%r, %r,
...)" % (outfile, hid))
+ for key in output_data.keys():
+ log.debug("About to call verify_dataset_correctness(...)
for output_data %r: %r" % (key, output_data.get(key)))
self.twill_test_case.verify_dataset_correctness( outfile,
hid=hid, attributes=attributes, shed_tool_id=shed_tool_id,
maxseconds=maxseconds )
def get_job_stream( self, history_id, output_data, stream ):
8 years, 6 months
shed tool dependencies
by Geert Vandeweyer
Hi,
Is there a default notation to specify perl modules (threading modules)
in a tool configuration or in a submission to the toolshed?
I've got some tools to share that make extensive use of these modules,
and they are not default in a perl distribution. Hence, I'd like to
inform the users that they need to install these modules (or that they
get installed by the the toolshed using cpan ?)
Best,
Geert
--
Geert Vandeweyer, Ph.D.
Department of Medical Genetics
University of Antwerp
Prins Boudewijnlaan 43
2650 Edegem
Belgium
Tel: +32 (0)3 275 97 56
E-mail: geert.vandeweyer(a)ua.ac.be
http://ua.ac.be/cognitivegenetics
http://www.linkedin.com/pub/geert-vandeweyer/26/457/726
8 years, 6 months
external user authentication
by Shrum, Donald C
I'm having some difficulty with external user authentication as described here -
https://wiki.galaxyproject.org/Admin/Config/ExternalUserDatbases
I've added these two lines to universe_wsgi.ini
use_remote_user = True
remote_user_maildomain = fsu.edu
I've setup ldap authentication in Apache and verified I have a value in REMOTE_USER with a simple php script...
RequestHeader set REMOTE_USER %{AUTHENTICATE_uid}e
This adds - REMOTE_USER: dcshrum
When I add in the rewrites and forward to galaxy on port 8080 I'm still getting:
Access to Galaxy is denied
Galaxy is configured to authenticate users via an external method (such as HTTP authentication in Apache), but a username was not provided by the upstream (proxy) server.....
Any help debugging this would be greatly appreciated. I'm running out of places to look!
--Donny
FSU Research Computing Center
8 years, 6 months
nginx upload
by Briand, Sheldon
Hi,
I'm trying to debug file uploads using the file browser. I have nginx setup to proxy but not to a sub directory.
/usr/sbin/nginx -V
nginx version: nginx/1.4.3
--add-module=/usr/local/src/nginx_upload_module-2.2.0
Here are the settings in my universe_wsgi.ini:
nginx_upload_store = database/tmp/upload_store
nginx_upload_path = /_upload
Here is the nginx config:
user galaxy;
worker_processes 1;
events {
worker_connections 1024;
}
http {
include /etc/nginx/mime.types;
default_type application/octet-stream;
gzip on;
gzip_http_version 1.1;
gzip_vary on;
gzip_comp_level 4;
gzip_proxied any;
gzip_types text/plain text/css application/x-javascript text/xml applicatio$
gzip_buffers 16 8k;
gzip_disable "MSIE [1-6].(?!.*SV1)";
upstream galaxy_app {
server localhost:8080;
}
log_format main '$remote_addr - $remote_user [$time_local] "$request" '
'$status $body_bytes_sent "$http_referer" '
'"$http_user_agent" "$http_x_forwarded_for"';
access_log /var/log/nginx/access.log main;
sendfile on;
keepalive_timeout 65;
server {
listen 80;
server_name localhost eugene.imb.nrc.ca;
client_max_body_size 10G;
#charset koi8-r;
#access_log /var/log/nginx/log/host.access.log main;
location / {
proxy_pass http://galaxy_app;
proxy_set_header X-Forwarded-Host $host;
proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
}
location /static {
alias /software/packages/galaxy/galaxy-dist/static;
expires 24h;
}
location /static/style {
alias /software/packages/galaxy/galaxy-dist/static/june_2007_style/blue;
expires 24h;
}
location /static/scripts {
alias /software/packages/galaxy/galaxy-dist/static/scripts/packed;
}
location /favicon.ico {
alias /software/packages/galaxy/galaxy_dist/static/favicon.ico;
}
location /robots.txt {
alias /software/packages/galaxy/galaxy-dist/static/robots.txt;
}
location /_x_accel_redirect/ {
internal;
alias /;
}
location /_upload {
upload_store /software/packages/galaxy/galaxy-dist/database/tmp/upload_store;
upload_pass_form_field "";
upload_set_form_field "__${upload_field_name}__is_composite" "true";
upload_set_form_field "__${upload_field_name}__keys" "name path";
upload_set_form_field "${upload_field_name}_name" "$upload_file_name";
upload_set_form_field "${upload_field_name}_path" "$upload_tmp_path";
upload_pass_args on;
upload_pass /_upload_done;
}
location /_upload_done {
set $dst /tool_runner/index;
if ($args ~ nginx_redir=([^&]+)) {
set $dst $1;
}
rewrite "" $dst;
}
error_page 500 502 503 504 /50x.html;
location = /50x.html {
root /usr/share/nginx/html;
}
The upload store is on a NFS filesystem. There is nothing in the nginx error log. There is nothing in the paster log. I've noticed that files start to be written to the upload store directory but get cut off by a refresh:
-----------------------------234101252030936
Content-Disposition: form-data; name="refresh"
refresh
The upload usually tries again ~10 times, unless manually cutoff earlier, before giving up. The user usually sees that the data is uploading and that message never goes away.
I should mention that I have not yet upgraded to the latest release:
$ hg summary
parent: 11216:c458a0fe1ba8
I also have debug settings on for galaxy.
Likely some setting I've messed up. I'd be grateful for a point in the right direction. I've looked through the archives and googled bunch without success.
I saw there have been changes to how the upload module works with nginx 1.3.9+. Should I downgrade my nginx if the newer version don't play nicely with galaxy?
Thanks,
-Sheldon
Sheldon Briand
NRC Research Computing Support Analyst
Research Computing Support / Soutien Informartique a la Recherche
Operations, Science Portfolio / Operations, Portefeuil des sciences
SSC-NRC / SPC-CNRC
Rm 329A, 1411 Oxford Street / Piece 329A, 1411 Rue Oxford
Halifax, NS B3H 3Z1
902 426-1677
sheldon.briand(a)ssc-spc.gc.ca
8 years, 6 months
popup window possible?
by Neil.Burdett＠csiro.au
Hi,
Is it possible to get a popup dialog box to appear for a tool? If so any examples on this please?
i.e. the popup may just give a warning or an info message etc... that the user can confirm before proceeding. Or maybe another way to achieve the same thing?
Thanks
Neil
Neil Burdett
Software Engineer | The Australian e-Health Research Centre
Computational Informatics
CSIRO
E: Neil.Burdett(a)csiro.au T: 07 3253 3626
Address: Level 5, UQ Health Science Building 901/16 Royal Brisbane and Women's Hospital, Herston, Brisbane, QLD, 4029
www.csiro.au | http://milxview.csiro.au
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setting up Galaxy for torque pbs
by Ketan Maheshwari
Hi,
I am trying to set up Galaxy to interface with a Cray system which runs
Torque/PBS.
After reading this Galaxy wiki page:
https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster#PBS
I was able to scramble torque egg with the following command:
LIBTORQUE_DIR=/opt/torque/2.4.11/lib/libtorque.so.2 python
scripts/scramble.py -e pbs_python
I do not fully understand the "parameters and configuration" part in PBS
section of the wiki page. Where exactly the "runner" XML snippet with
<plugin> and <destinations> should be placed?
Also wondering if the snippet will be required for all tools that I want to
run on compute nodes or is it a global setting? Can I tell existing tools
to use this setup?
Another question is, can I configure Galaxy to submit jobs to compute
cluster as a mortal user and not an admin of the system?
Thanks,
--
Ketan
8 years, 6 months
History panel filters
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Dear Galaxy devs,
I apologize if somebody has already proposed this idea.
I think that it would be great to have a filter for the history panel based
on name, data type and so on similar to the one on the tools panel. I
really feel the need of it when working on histories with many datasets.
Federico Zambelli
8 years, 6 months
migrate_tools error with latest release (hg update release_2014.02.10 )
by Geert Vandeweyer
Hi,
I'm having problems upgrading Galaxy to the latest release. The migrate
tools script gives the following error.
No handlers could be found for logger "galaxy.tools"
Traceback (most recent call last):
File "./scripts/migrate_tools/migrate_tools.py", line 21, in <module>
app = MigrateToolsApplication( sys.argv[ 1 ] )
File
"/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/migrate/common.py",
line 45, in __init__
self.installed_repository_manager =
installed_repository_manager.InstalledRepositoryManager( self )
File
"/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/installed_repository_manager.py",
line 66, in __init__
self.load_dependency_relationships()
File
"/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/installed_repository_manager.py",
line 269, in load_dependency_relationships
self.add_entry_to_runtime_tool_dependencies_of_installed_tool_dependencies(
tool_dependency )
File
"/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/installed_repository_manager.py",
line 147, in
add_entry_to_runtime_tool_dependencies_of_installed_tool_dependencies
tool_dependency_util.get_runtime_dependent_tool_dependency_tuples(
self.app, tool_dependency, status=None )
File
"/galaxy/galaxy-dist/lib/tool_shed/util/tool_dependency_util.py", line
323, in get_runtime_dependent_tool_dependency_tuples
env_shell_file_path = td.get_env_shell_file_path( app )
File
"/galaxy/galaxy-dist/lib/galaxy/model/tool_shed_install/__init__.py",
line 533, in get_env_shell_file_path
installation_directory = self.installation_directory( app )
File
"/galaxy/galaxy-dist/lib/galaxy/model/tool_shed_install/__init__.py",
line 548, in installation_directory
self.tool_shed_repository.owner,
AttributeError: 'NoneType' object has no attribute 'owner'
Any help on how to resolve this?
The 0009_tools.xml content is :
<?xml version="1.0"?>
<toolshed name="toolshed.g2.bx.psu.edu">
<repository owner="devteam" changeset_revision="96d2e31a3938"
name="bowtie2" description="Bowtie2">
<tool id="bowtie2" version="0.2" file="bowtie2_wrapper.xml" />
</repository>
<repository owner="devteam" changeset_revision="a0c8dc671a23"
name="ccat" description="Control-based ChIP-seq Analysis Tool">
<tool id="peakcalling_ccat" version="0.0.1"
file="ccat_wrapper.xml" />
</repository>
<repository owner="devteam" changeset_revision="7cc64024fe92"
name="clustalw" description="ClustalW multiple sequence alignment
program for DNA or proteins">
<tool id="clustalw" version="0.1" file="rgClustalw.xml" />
</repository>
<repository owner="devteam" changeset_revision="6708501767b6"
name="dwt_cor_ava_perclass" description="Compute P-values and
Correlation Coefficients for Feature Occurrences">
<tool
id="compute_p-values_correlation_coefficients_feature_occurrences_between_two_datasets_using_discrete_wavelet_transfom"
version="1.0.0" file="execute_dwt_cor_aVa_perClass.xml" />
</repository>
<repository owner="devteam" changeset_revision="0f2eda4ea8dc"
name="dwt_cor_avb_all" description="Compute P-values and Correlation
Coefficients for Occurrences of Two Set of Features">
<tool
id="compute_p-values_correlation_coefficients_featureA_featureB_occurrences_between_two_datasets_using_discrete_wavelet_transfom"
version="1.0.0" file="execute_dwt_cor_aVb_all.xml" />
</repository>
<repository owner="devteam" changeset_revision="0b89b03ad760"
name="dwt_ivc_all" description="Compute P-values and Second Moments for
Feature Occurrences">
<tool
id="compute_p-values_second_moments_feature_occurrences_between_two_datasets_using_discrete_wavelet_transfom"
version="1.0.0" file="execute_dwt_IvC_all.xml" />
</repository>
<repository owner="devteam" changeset_revision="cb422b6f49d2"
name="dwt_var_perclass" description="Compute P-values and Max Variances
for Feature Occurrences">
<tool
id="compute_p-values_max_variances_feature_occurrences_in_one_dataset_using_discrete_wavelet_transfom"
version="1.0.0" file="execute_dwt_var_perClass.xml" />
</repository>
<repository owner="devteam" changeset_revision="d56c5d2e1a29"
name="dwt_var_perfeature" description="Wavelet variance using Discrete
Wavelet Transfoms">
<tool id="dwt_var1" version="1.0.0"
file="execute_dwt_var_perFeature.xml" />
</repository>
<repository owner="devteam" changeset_revision="7b0708761d05"
name="express" description="Quantify the abundances of a set of target
sequences from sampled subsequences">
<tool id="express" version="1.1.1" file="express_wrapper.xml" />
</repository>
<repository owner="devteam" changeset_revision="e28c965eeed4"
name="fastqc" description="Read QC reports using FastQC">
<tool id="fastqc" version="1.0.0" file="rgFastQC.xml" />
</repository>
<repository owner="devteam" changeset_revision="94306bdd58f7"
name="fastq_combiner" description="Combine FASTA and QUAL into FASTQ.">
<tool id="fastq_combiner" version="1.0.1"
file="fastq_combiner.xml" />
</repository>
<repository owner="devteam" changeset_revision="30d9ece6c752"
name="fastq_filter" description="Filter FASTQ reads by quality score and
length">
<tool id="fastq_filter" version="1.0.0" file="fastq_filter.xml" />
</repository>
<repository owner="devteam" changeset_revision="1298445c852b"
name="fastq_groomer" description="Convert between various FASTQ quality
formats.">
<tool id="fastq_groomer" version="1.0.4"
file="fastq_groomer.xml" />
</repository>
<repository owner="devteam" changeset_revision="5d1e9e13e8db"
name="fastq_manipulation" description="Manipulate FASTQ reads on various
attributes.">
<tool id="fastq_manipulation" version="1.0.1"
file="fastq_manipulation.xml" />
</repository>
<repository owner="devteam" changeset_revision="5a7b5751617b"
name="fastq_masker_by_quality" description="FASTQ Masker by quality score">
<tool id="fastq_masker_by_quality" version="1.0.0"
file="fastq_masker_by_quality.xml" />
</repository>
<repository owner="devteam" changeset_revision="f0949bc49926"
name="fastq_paired_end_deinterlacer" description="FASTQ de-interlacer on
paired end reads.">
<tool id="fastq_paired_end_deinterlacer" version="1.1"
file="fastq_paired_end_deinterlacer.xml" />
</repository>
<repository owner="devteam" changeset_revision="b89bdf6acb6c"
name="fastq_paired_end_interlacer" description="FASTQ interlacer on
paired end reads">
<tool id="fastq_paired_end_interlacer" version="1.1"
file="fastq_paired_end_interlacer.xml" />
</repository>
<repository owner="devteam" changeset_revision="2793d1d765b9"
name="fastq_paired_end_joiner" description="FASTQ joiner on paired end
reads">
<tool id="fastq_paired_end_joiner" version="1.0.0"
file="fastq_paired_end_joiner.xml" />
</repository>
<repository owner="devteam" changeset_revision="c549e99026db"
name="fastq_paired_end_splitter" description="FASTQ splitter on joined
paired end reads">
<tool id="fastq_paired_end_splitter" version="1.0.0"
file="fastq_paired_end_splitter.xml" />
</repository>
<repository owner="devteam" changeset_revision="9b7b4e0ca9db"
name="fastq_stats" description="FASTQ Summary Statistics by column">
<tool id="fastq_stats" version="1.0.0" file="fastq_stats.xml" />
</repository>
<repository owner="devteam" changeset_revision="3571553aeb20"
name="fastqtofasta" description="FASTQ to FASTA converter">
<tool id="fastq_to_fasta_python" version="1.0.0"
file="fastq_to_fasta.xml" />
</repository>
<repository owner="devteam" changeset_revision="bc9269529e88"
name="fastq_to_tabular" description="FASTQ to Tabular converter">
<tool id="fastq_to_tabular" version="1.1.0"
file="fastq_to_tabular.xml" />
</repository>
<repository owner="devteam" changeset_revision="0b9feb0ed628"
name="fastq_trimmer" description="FASTQ Trimmer by quality">
<tool id="fastq_trimmer" version="1.0.0"
file="fastq_trimmer.xml" />
</repository>
<repository owner="devteam" changeset_revision="1cdcaf5fc1da"
name="fastq_trimmer_by_quality" description="FASTQ Quality Trimmer by
sliding window">
<tool id="fastq_quality_trimmer" version="1.0.0"
file="fastq_trimmer_by_quality.xml" />
</repository>
<repository owner="devteam" changeset_revision="31154ff9f5e1"
name="filter_transcripts_via_tracking" description="Filter Combined
Transcripts">
<tool id="filter_combined_via_tracking" version="0.1"
file="filter_transcripts_via_tracking.xml" />
</repository>
<repository owner="devteam" changeset_revision="acf51ff24c7d"
name="find_diag_hits" description="Identify sequence reads corresponding
to a particular taxonomic group">
<tool id="find_diag_hits" version="1.0.0"
file="find_diag_hits.xml" />
</repository>
<repository owner="devteam" changeset_revision="33a0e6aca936"
name="freebayes_wrapper" description="Call SNPS with Freebayes">
<tool id="freebayes_wrapper" version="0.5.0"
file="freebayes.xml" />
</repository>
<repository owner="devteam" changeset_revision="7b1b03c4465d"
name="gi2taxonomy" description="Fetch taxonomic representation">
<tool id="Fetch Taxonomic Ranks" version="1.1.0"
file="gi2taxonomy.xml" />
</repository>
<repository owner="devteam" changeset_revision="2cd5ee197ec7"
name="gmaj" description="GMAJ Multiple Alignment Viewer">
<tool id="gmaj_1" version="2.0.1" file="GMAJ.xml" />
</repository>
<repository owner="devteam" changeset_revision="33e8ed5a4601"
name="lca_wrapper" description="Find lowest diagnostic rank">
<tool id="lca1" version="1.0.1" file="lca.xml" />
</repository>
<repository owner="devteam" changeset_revision="ae2ec275332a"
name="macs" description="Model-based Analysis of ChIP-Seq">
<tool id="peakcalling_macs" version="1.0.1"
file="macs_wrapper.xml" />
</repository>
<repository owner="devteam" changeset_revision="8cd5945559b8"
name="poisson2test" description="Poisson two-sample test">
<tool id="poisson2test" version="1.0.0" file="poisson2test.xml" />
</repository>
<repository owner="devteam" changeset_revision="82a8234e03f2"
name="sicer" description="Statistical approach for the Identification of
ChIP-Enriched Regions">
<tool id="peakcalling_sicer" version="0.0.1"
file="sicer_wrapper.xml" />
</repository>
<repository owner="devteam" changeset_revision="9e2b9ca7f33a"
name="t2ps" description="Draw phylogeny">
<tool id="Draw_phylogram" version="1.0.0"
file="t2ps_wrapper.xml" />
</repository>
<repository owner="devteam" changeset_revision="592acb9505fc"
name="t2t_report" description="Summarize taxonomy">
<tool id="t2t_report" version="1.0.0" file="t2t_report.xml" />
</repository>
<repository owner="devteam" changeset_revision="b334cd1095ea"
name="tabular_to_fastq" description="Tabular to FASTQ converter">
<tool id="tabular_to_fastq" version="1.0.0"
file="tabular_to_fastq.xml" />
</repository>
<repository owner="devteam" changeset_revision="1030acbecce6"
name="tophat" description="Find splice junctions using RNA-seq data">
<tool id="tophat" version="1.5.0" file="tophat_wrapper.xml" />
</repository>
<repository owner="devteam" changeset_revision="ffa30bedbee3"
name="tophat2" description="Gapped-read mapper for RNA-seq data">
<tool id="tophat2" version="0.6" file="tophat2_wrapper.xml" />
</repository>
<repository owner="devteam" changeset_revision="b001b50f2009"
name="vcf_annotate" description="Annotate a VCF file (dbSNP, hapmap)">
<tool id="vcf_annotate" version="1.0.0" file="annotate.xml" />
</repository>
<repository owner="devteam" changeset_revision="76ad0b7865b9"
name="vcf_extract" description="Extract reads from a specified region">
<tool id="vcf_extract" version="1.0.0" file="extract.xml" />
</repository>
<repository owner="devteam" changeset_revision="da1a6f33b504"
name="vcf_filter" description="Filter a VCF file">
<tool id="vcf_filter" version="1.0.0" file="filter.xml" />
</repository>
<repository owner="devteam" changeset_revision="9d162bde4113"
name="vcf_intersect" description="Generate the intersection of two VCF
files">
<tool id="vcf_intersect" version="1.0.0"
file="vcf_tools/intersect.xml" />
</repository>
<repository owner="devteam" changeset_revision="66253fc0a69b"
name="weblogo3" description="Sequence Logo generator for fasta (eg
Clustal alignments)">
<tool id="rgweblogo3" version="0.4" file="rgWebLogo3.xml" />
</repository>
</toolshed>
Best,
Geert
--
Geert Vandeweyer, Ph.D.
Department of Medical Genetics
University of Antwerp
Prins Boudewijnlaan 43
2650 Edegem
Belgium
Tel: +32 (0)3 275 97 56
E-mail: geert.vandeweyer(a)ua.ac.be
http://ua.ac.be/cognitivegenetics
http://www.linkedin.com/in/geertvandeweyer
8 years, 6 months
Error installing VarScan from Toolshed
by graham etherington (TSL)
Hi,
I’m trying to install VarScan from the Main Toolshed. I’ve tried both the versions available (‘varscan’ from fcaramia and ‘varscan_version_2’ from devteam), but I get the same error each time:
File "/tsl/services/galaxy/dist/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py", line 294, in install_and_build_package_via_fabric fabric_util.install_and_build_package( app, tool_dependency, actions_dict )
File "/tsl/services/galaxy/dist/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py", line 619, in install_and_build_package destination=full_path_to_dir )
File "/usr/lib64/python2.6/contextlib.py", line 34, in __exit__ self.gen.throw(type, value, traceback)
File "/tsl/services/galaxy/dist/galaxy-dist/eggs/Fabric-1.7.0-py2.6.egg/fabric/context_managers.py", line 142, in _setenv yield
File "/tsl/services/galaxy/dist/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py", line 309, in install_and_build_package dir = td_common_util.url_download( work_dir, downloaded_filename, url, extract=True )
File "/tsl/services/galaxy/dist/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py", line 434, in url_download archive = CompressedFile( file_path )
File "/tsl/services/galaxy/dist/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py", line 27, in __init__ self.type = self.file_type 'CompressedFile' object has no attribute 'file_type'
Can anyone suggest what might be going wrong here?
Many thanks,
Graham
Dr. Graham Etherington
Bioinformatics Support Officer,
The Sainsbury Laboratory,
Norwich Research Park,
Norwich NR4 7UH.
UK
Tel: +44 (0)1603 450601
8 years, 6 months
