Re: [galaxy-dev] FTP upload - symlink to uploaded data

2012-08-22 Thread Joachim Jacob
Hi Nate, I have set the new_file_path to the FTP upload directory as you suggested. new_file_path=/mnt/galaxydb/ftp This did not succeed however: still there is copying to the /tmp directory. I also see that importing data sets into data libraries from a directory of files behaves

[galaxy-dev] ToolShed enhancement for repository lists

2012-08-22 Thread Peter Cock
Hi all, This is an idea I mentioned to Dannon (off list during discussion about moving the NCBI BLAST+ wrappers to the Tool Shed), and he seemed positive about it. Currently the left hand pane of the ToolShed (once logged in) looks like this: Search * Search for valid tools * Search for

Re: [galaxy-dev] admin_user not being seen

2012-08-22 Thread Paul-Michael Agapow
A peculiar quirk - I'm configuring a new Galaxy system for production use and can't get it to recognise my account as an admin, i.e. the admin menu doesn't appear after I've added my email address to the admin_user line in the universe file. Of course, I've restarted the instance multiple

[galaxy-dev] missing slash when installing from toolshed?

2012-08-22 Thread Dan Sullivan
Hi, Galaxy Developers, I have a question that is very similar to the following thread; http://dev.list.galaxyproject.org/Problem-fetching-updates-to-toolshed-tool-td4353417.html Basically whenever I try to install a tool from the toolshed, it appears that a trailing slash is not appended to

Re: [galaxy-dev] galaxy-dev Digest, Vol 74, Issue 21

2012-08-22 Thread Adhemar
Here is a copy of the whole VirtualHost section. Thanks, Adhemar VirtualHost lbas046.cnptia.embrapa.br:443 ServerName lbas046.cnptia.embrapa.br ErrorLog logs/galaxy_ssl_error_log TransferLog logs/galaxy_ssl_access_log LogLevel warn SSLEngine on SSLCertificateFile

Re: [galaxy-dev] [galaxy-user] LimitInternalRecursion

2012-08-22 Thread Adhemar
Here is a copy of the whole VirtualHost section. Thanks, Adhemar VirtualHost lbas046.cnptia.embrapa.br:443 ServerName lbas046.cnptia.embrapa.br ErrorLog logs/galaxy_ssl_error_log TransferLog logs/galaxy_ssl_access_log LogLevel warn SSLEngine on SSLCertificateFile

Re: [galaxy-dev] [galaxy-user] LimitInternalRecursion

2012-08-22 Thread Scott McManus
It's the last rewrite rule that's causing the infinite recursion: RewriteRule ^/galaxy(.*) http://localhost:8080$1 [P] Check out this link: http://httpd.apache.org/docs/current/mod/mod_rewrite.html#rewriterule Look for the table of given rules and resulting substitutions - the proxying

Re: [galaxy-dev] [galaxy-user] LimitInternalRecursion

2012-08-22 Thread Nate Coraor
Hi Adhemar, Could you try the following?: VirtualHost lbas046.cnptia.embrapa.br:443 ServerName lbas046.cnptia.embrapa.br ErrorLog logs/galaxy_ssl_error_log TransferLog logs/galaxy_ssl_access_log LogLevel warn SSLEngine on SSLCertificateFile

Re: [galaxy-dev] [galaxy-user] LimitInternalRecursion

2012-08-22 Thread Adhemar
Hi Nate! That line really solved the problem. RewriteCond %{IS_SUBREQ} ^false$ No more errors in my log! Thank you, I really appreciate it. Adhemar 2012/8/22 Nate Coraor n...@bx.psu.edu Hi Adhemar, Could you try the following?: VirtualHost lbas046.cnptia.embrapa.br:443

[galaxy-dev] patch for vcf QUAL field with missing value . in lib/galaxy/visualization/tracks/data_providers.py

2012-08-22 Thread Jim Johnson
The VCF format ( http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41 ) specifies . to represent missing values. lib/galaxy/visualization/tracks/data_providers.py throws an float conversion error when the qual field of a vcf file has the