Re: [galaxy-dev] Turn your workflow into a tool?

Hi Alexander, Thanks for the reminder to get that info posted - is about 95% done. Plus I decided just now to add a bit about sharing to this same page. I'll have this part done tomorrow, and will work on getting the rest of this wiki area polished near term (updates + unpublished tutorials). For

[galaxy-dev] BUG: Collections and History export

Hi, when downloading/exporting a history via the interface, visible collections are not being exported. The contents of the collection(s) are hidden, the Colleciton itself is visible. Best, Alexander ___ Please keep all replies on the list

Re: [galaxy-dev] Turn your workflow into a tool?

awesome! that worked! Now I can also see the Page ;) Will such a shown workflow be visible for all users? If not, is is possible to make it visible to all users? Thanks, Alexander 2015-09-02 12:02 GMT-05:00 Jennifer Hillman-Jackson : > Hello, > > Go the the Worflows home page by clicking on the

Re: [galaxy-dev] ProFTPd in CloudMan

Great! Thanks! 2015-09-02 8:47 GMT-05:00 Enis Afgan : > Thanks for reporting this (and figuring out the solution). It's been fixed > with this commit > > so any new cluster will work fine. > > Cheers. > >

Re: [galaxy-dev] LDAP Auto register - "username is None"

Hi Martin, I suspect there's an error in the sample auth_conf.xml file, should try to match only the email, not the username (unless you specify True, in which case it's viceversa) because it is not known when you first login. In fact, for ActiveDirectory the filter is: (&(objectClass=user)(

Re: [galaxy-dev] Turn your workflow into a tool?

Hello, Go the the Worflows home page by clicking on the link in the upper masthead. On the bottom of that page, in the section 'Other options' click on the button 'Configure your workflow menu'. The next page lists all of your workflows. To place any at the top of your workflow list (found at the

Re: [galaxy-dev] about galaxy

There are multiple fastq formats and some tools only accept a subset of it. Please have a look at the 'FASTQ Groomer' tool it should allow you to convert your datase to the fastq format you need. Thank you for using Galaxy Martin On Wed, Sep 2, 2015 at 12:52 PM Dong Liu wrote: > Dear Galaxy >

Re: [galaxy-dev] about galaxy

Hello, The datatype 'fastqsanger' needs to be assigned. See the Galaxy Support wiki for how to do this (and for how to double check if the type is correct): https://wiki.galaxyproject.org/Support#Tool_doesn.27t_recognize_dataset Thanks for using Galaxy, Jen -- Jennifer Hillman-Jackson Galaxy Ap

[galaxy-dev] about galaxy

Dear Galaxy I am a new user on Galaxy online service. When I uploaded my data file in fastq form, the utility of Galaxy such as NGS:QC and manipulation, FastQC and Trim sequences can not be availabe. I dont why. can you tell me how to use Galaxy using my data? Dong Liu visiting scholar at

Re: [galaxy-dev] LDAP Auto register - "username is None"

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Nicola, It's an OpenLDAP server. uid isn't set on ours, it's cn instead, so using ldapsearch I can correctly bind; dn: cn=mjv08,ou=Person,dc=dc1,dc=example,dc=com objectClass: aberPerson cn: mjv08 So authentication to the ldap server is working,

Re: [galaxy-dev] LDAP Auto register - "username is None"

Hi Martin, what LDAP server are you using? We have tested only OpenLDAP and ActiveDirectory, but should work on any LDAP server. If it is OpenLDAP, I think you should use: uid,mail (&(mail={email})(uid={username})) {uid} More details in: https://github.com/galaxyproject/galaxy/blob/dev/config/

[galaxy-dev] PBS Torque 15007: No permission

Hello All, I have Galaxy running on the latest version of Biolinux configured to work with PBS/Torque version Version: 4.2.8, all jobs are being submitted as Debian-galaxy (This is a global user in the cluster and a local user on the Biolinux box). Whenever we submit a job we get the error b

Re: [galaxy-dev] ProFTPd in CloudMan

Thanks for reporting this (and figuring out the solution). It's been fixed with this commit so any new cluster will work fine. Cheers. On Tue, Sep 1, 2015 at 7:42 PM, Alexander Vowinkel < vowinkel.alexan..

Re: [galaxy-dev] Wiki documentation for tool_dependencies.xml file

Tricky, thanks for updating the wiki! On 02.09.2015 15:23, Peter Cock wrote: Thanks Bjoern, Yes, reading the code in that file all three do look to be created via os.path.abspath(...) and so won't have a trailing slash. I've added that information to the wiki. I'm assuming this now in my MIRA

Re: [galaxy-dev] Wiki documentation for tool_dependencies.xml file

Thanks Bjoern, Yes, reading the code in that file all three do look to be created via os.path.abspath(...) and so won't have a trailing slash. I've added that information to the wiki. I'm assuming this now in my MIRA 4.9.5 package, but a double trailing slash should be harmless anyway: https://g

Re: [galaxy-dev] Wiki documentation for tool_dependencies.xml file

Hi Peter, it looks like they are without the trailing slash: https://github.com/galaxyproject/galaxy/blob/dev/lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py#L598 https://github.com/galaxyproject/galaxy/pull/511/files#diff-93a0802a2778786e35399ed83453dca6R48 Ciao, Bjoern

[galaxy-dev] LDAP Auto register - "username is None"

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi All, I've been trying to get the new LDAP module to work. It works fine for existing users but I can't get auto-register to work. In the logs I can see the successful logins look like this; galaxy.webapps.galaxy.controllers.user DEBUG 2015-09-02

Re: [galaxy-dev] Wiki documentation for tool_dependencies.xml file

Lovely, thanks! I've added a couple of links pointing to that page :) It does list a few of relevant environment variables, $INSTALL_DIR, $REPOSITORY_INSTALL_DIR and $TMP_WORK_DIR, but does not comment on if these directory names include a trailing slash or not... Peter On Wed, Sep 2, 2015 at 12

Re: [galaxy-dev] Renaming pages on the Galaxy wiki

Hi Peter, the wiki uses MoinMoin. As explained in https://moinmo.in/HelpOnProcessingInstructions#A.23redirect you can just create a new page with the old name containing only: #redirect NewWikiPageName I've already done that for the page you moved. Cheers, Nicola Il 02.09.2015 12:28 Peter

Re: [galaxy-dev] Wiki documentation for tool_dependencies.xml file

Hi Peter, the page you are looking for is: https://wiki.galaxyproject.org/ToolDependenciesTagSets I think it should be better linked, I had to bookmark it! Cheers, Nicola Il 02.09.2015 12:33 Peter Cock ha scritto: > Hi all, > > Is there a page on the wiki describing the tool_dependencies.x

Re: [galaxy-dev] Installing Cairo into Gakaxy

I am still having issues installing Cairo into R I have tracked part of the problem down to: https://depot.galaxyproject.org/package/linux/x86_64/R/R-3.2.1-Linux-x86_64.tgz does have any include files so no headers. https://testtoolshed.g2.bx.psu.edu/view/iuc/package_r_3_2_1/3d28600fc82c has:

[galaxy-dev] Wiki documentation for tool_dependencies.xml file

Hi all, Is there a page on the wiki describing the tool_dependencies.xml file syntax? Searching finds pages with examples, e.g. https://wiki.galaxyproject.org/ToolsWithDependenciesInSameRepository https://wiki.galaxyproject.org/ComplexRepositoryDependencies What I am looking for is something lik

[galaxy-dev] Renaming pages on the Galaxy wiki

Hi all, I just renamed a page on the wiki to fix a typo: https://wiki.galaxyproject.org/ToolsWitDependenciesInSameRepository now: https://wiki.galaxyproject.org/ToolsWithDependenciesInSameRepository I didn't see any option about setting up a redirection from the old URL (for pages linked to it