Galaxy Development List Archive

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Galaxy Project

Archive for the Galaxy-Dev mailing list. If you have a question about deploying, enhancing, tuning or adding to a Galaxy instance then this is a good place to find an answer.

Galaxy is an open, web-based platform for accessible, reproducible, and transparent computational biomedical research.

  • Accessibility: Galaxy enables users without programming experience to easily specify parameters and run tools and workflows.
  • Reproducibility: Galaxy captures all information necessary so that any user can repeat and understand a complete computational analysis.
  • Transparency: Galaxy enables users to share and publish analyses via the web and create Pages--interactive, web-based documents that describe a complete analysis.
Galaxy is open source for all organizations. The public Galaxy server makes analysis tools, genomic data, tutorial demonstrations, persistent workspaces, and publication services available to any scientist that has access to the Internet. Local Galaxy servers can be set up by downloading the Galaxy application and customizing it to meet particular needs.


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Topics (9170)
Replies Last Post Views
snpEff and java issue by Iry Witham
0
by Iry Witham
snpeff tool for Galaxy extra_files_path by Jim Johnson-3
7
by Jim Johnson-3
Set output dbkey from parameter value by Nikos Sidiropoulos
4
by Nikos Sidiropoulos
UCSC Main table browser by Shrum, Donald C
1
by John Chilton-4
Assertion errors when starting Galaxy by ricky_pz2
0
by ricky_pz2
Galaxy database corrupted by tchu
0
by tchu
CloudMan with HTCondor and Slurm & mounting pathes by azab
1
by Enis Afgan-2
error running API with example_watch_folder.py by burdettn
2
by John Chilton-4
failure to export workflows by Wolfgang Maier
6
by Wolfgang Maier
missing "fastq groomer" tool on galaxy cloudman by NAMIT KUMAR
2
by Masoumeh Sikaroodi
quick note of thanks by Chris Dagdigian
1
by Dannon Baker-2
API : Max retries exceeded by Gildas Le Corguillé
3
by Gildas Le Corguillé
GATK2 java version related issues by Iry Witham
2
by Iry Witham
Why does Galaxy CloudMan 2.3 (ami-a7dbf6ce) run the boinc client? by Chris Dagdigian
1
by Dannon Baker-2
Anyone else having issues with cloudman cloudlaunch? by Chris Dagdigian
5
by Chris Dagdigian
Tool development: Is it possible to pass a user's id in dynamic_options() parameter? by Dooley, Damion
3
by Daniel Blankenberg
Is it possible to condition tool wrappers on external inputs? by Melissa Cline
1
by Daniel Blankenberg
Data uploaded with new upload tool doesn't get added to history by Peter van Heusden
4
by Dannon Baker-2
SQLalchemy InvalidRequestError by Ulf
7
by Dannon Baker-2
snpEf dataset generation errors by Iry Witham
0
by Iry Witham
CloudMan: Autoscaling =Unable to run this job due to a cluster error by rpetit
3
by Enis Afgan-2
Download tool-dependency with using a proxy and functional tests http 403 error by meisterJaeger
1
by John Chilton-4
GATK2 reporting "Invalid argument value '/mnt/galaxy/tools/gatk2/bin/' at position 8." by Iry Witham
0
by Iry Witham
no universe_wsgi.ini & can't install tools from the standard toolshed because: "Initializing repository installation failed" by Chris Dagdigian
4
by John Chilton-4
ToolShed tool preview broken (TestToolShed too) by Peter Cock
1
by Peter Cock
testtoolshed internal server error by Stef van Lieshout
3
by Peter Cock
Internal Server Error on metadata reset by saketkc
1
by Martin Čech
Cloudman indices installation/configuration by Iry Witham
7
by Björn Grüning-3
clustalomega from toolshed installation issue by Isabelle Phan
2
by Isabelle Phan
Apache proxy, SSL, and UCSC get data by Lance Parsons
0
by Lance Parsons
Central tool shed installations fail due to redirect by Kandalaft, Iyad
1
by Kandalaft, Iyad
installing R bioconductor package DNAcopy gfortran setup_r_environment by Stef van Lieshout
0
by Stef van Lieshout
CfP: Reproducible Science Hackathon - Curriculum & Workflow Development by Tracy K. Teal
0
by Tracy K. Teal
Get Data - url upload (connection timed out) by elchia
2
by elchia
Simple standard for API use of a global user/key that all loaded tools can draw upon? by Dooley, Damion
3
by Dooley, Damion
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