Set yourself up as a Galaxy admin, in universe_wsgi.ini, add your galaxy account ( email ) to the following: # this should be a comma-separated list of valid Galaxy users admin_users = you@youremail.edu You'll see an Admin link in the top Galaxy menu bar when you restart your Galaxy sever after making this change. Click on it, and you be presented with teh Galaxy Admin UI. Look for the "Manage data libraries" link in th left panel, create a new data library, and you can upload datasets to using 1 of 4 options, including this latest option just introduced. Greg Von Kuster Galaxy Development Team Abhishek Pratap wrote:
I think that could be it. I am using the "Upload File " option under the "Get Data" from the left hand menu. Sorry for the confusion if I am doing something that I am not supposed to. How do we upload data to data library ?
-Abhi
On Fri, Oct 2, 2009 at 3:46 PM, Greg Von Kuster <ghv2@psu.edu> wrote:
Ok, you have the change set.  Perhaps you are trying to upload into a history rather than a Data Library?  This new feature is only available for uploading into a Data Library.  Can you confirm?  I'm not sure what else could be causing you to not see the 4 options on the drop-down menu for uploading dataset into a Data Library.
Greg
Abhishek Pratap wrote:
Here it is :
hg heads
changeset:   2824:d97f4e86be45 tag:         tip parent:      2823:2c0c81150dbd parent:      2821:04a753865407 user:        Anton Nekrutenko <anton@bx.psu.edu> date:        Fri Oct 02 11:02:14 2009 -0400 summary:     merge
-Abhi
On Fri, Oct 2, 2009 at 3:30 PM, Greg Von Kuster <ghv2@psu.edu> wrote:
Please type the following in your galaxy install directory, and let me know what you get:
hg heads
Thanks
Abhishek Pratap wrote:
Hi Greg
Unfortunately it is not working for me. I made sure I cleared my browser cache before re-viewing it.
I have set the option as suggested by you in the universe_wsgi.ini file.
-Abhi
On Fri, Oct 2, 2009 at 2:53 PM, Greg Von Kuster <ghv2@psu.edu> wrote:
Hello Abhishek,
Add this to your universe_wsgi.ini file:
allow_library_path_paste = True
Then, clicking the down-arrow on the upload form
Create new data library datasets  ▼
will give you 4 options, 1 of which is:
Upload files from file system paths
Greg Von Kuster Galaxy Development Team
Abhishek Pratap wrote: > Hi Greg > > I have updated my galaxy rep to changeset 2825. I dont see the > checkbox on the "Upload File" page. Am I missing something ? > > Thanks, > -Abhi > > On Fri, Oct 2, 2009 at 10:21 AM, Greg Von Kuster <ghv2@psu.edu> wrote: >> Change set 2812 will be included in a release to the distribution >> today >> - >> here are details of a new option that we're hoping will provide what >> is >> needed for most labs. >> >> Add a new option, 'allow_library_path_paste' that adds a new upload >> page >> ("Upload files from file system paths") to the admin-side library >> upload >> pages. >> This form contains a textarea that allows Galaxy admins to paste any >> number >> of >> file system paths (files or directories) from which Galaxy will >> import >> library >> datasets, saving the directory structure (if desired). >>  Since such >> ability >> allows admins access to any file on the Galaxy server which is >> readable >> by >> Galaxy's system user, this option is disabled by default, and system >> administrators should take care in assigning Galaxy administrators >> when >> this >> feature is enabled.  Controls on what files are accessible >> to this >> tool >> based >> on ownership or other properties can be added at a later date if >> there >> is >> sufficient interest for such features. >> >> This commit also includes a checkbox on the "Upload directory of >> files" >> page >> (as well as the new "Upload files from file system paths" page above) >> that >> will >> prevent Galaxy from copying data to its files directory (by default, >> 'database/files/').  This is useful for large library >> datasets that >> live >> in >> their own managed locations on the file system, this will prevent the >> existence >> of duplicate copies of datasets (but means administrators must take >> care >> to >> manage data - moving or removing the data from its Galaxy-external >> location >> will render these datasets invalid within Galaxy). >> >> One unique feature to be aware of: when using the "Copy data into >> Galaxy?" >> checkbox on the "Upload directory of files" page, any symbolic links >> encountered in the chosen import directory will be made absolute and >> dereferenced ONCE.  This allows administrators to link >> large >> datasets to >> the >> import directory, rather than having to make full copies, while being >> able >> to >> delete such links after importing.  Only the first symlink >> (the one >> in >> the >> import directory itself) is dereferenced; all others remain. >>  See >> the >> following >> for an example: >> >> library_import_dir = /galaxy/import >> >> % ls -lR /galaxy/import >> /galaxy/import: >> total 6 >> drwxr-xr-x   2 nate     nate >>         512 >> Oct  1 11:31 link/ >> >> /galaxy/import/link: >> total 10 >> lrwxrwxrwx   1 nate     nate >>         >>  71 Oct  1 10:38 1.bed -> >> ../../../home/nate/galaxy/test-data/1.bed >> lrwxrwxrwx   1 nate     nate >>         >>  60 Oct  1 10:38 2.bed -> >> /home/nate/galaxy/test-data/2.bed >> lrwxrwxrwx   1 nate     nate >>         >>  11 Oct  1 10:38 3.bed -> >> ../../3.bed >> lrwxrwxrwx   1 nate     nate >>         >>  35 Oct  1 11:30 4.bed -> >> ../../galaxy_symlink/test-data/4.bed >> lrwxrwxrwx   1 nate     nate >>         >>  41 Oct  1 11:31 5.bed -> >> /galaxy/galaxy_symlink/test-data/5.bed >> >> % ls -l /galaxy/3.bed >> lrwxrwxrwx   1 nate     nate >>         >>  60 Oct  1 10:39 >> /galaxy/3.bed -> >> /home/nate/galaxy/test-data/3.bed >> >> % ls -l /galaxy/galaxy_symlink >> lrwxrwxrwx   1 nate     nate >>         >>  44 Oct  1 11:30 >> /galaxy/galaxy_symlink >> -> /home/nate/galaxy/ >> >> In this example, >> >> 1.bed is a relative symbolic link to the real 1.bed. >> >> 2.bed is an absolute symlink to the real 2.bed. >> >> 3.bed is a relative symlink to ../../3.bed, aka /galaxy/3.bed, which >> itself >> is >> a symlink to the real 3.bed. >> >> 4.bed is a relative symlink which follows another symlink >> (/galaxy/galaxy_symlink) to the real 4.bed. >> >> 5.bed is an absolute symlink in the same fashion as 4.bed >> >> If the 'link' server directory is chosen on the "Upload directory of >> files" >> page, and "Copy data into Galaxy?" is checked "No", the following >> files >> will >> be >> referenced by Galaxy: >> >> /home/nate/galaxy/test-data/1.bed >> /home/nate/galaxy/test-data/2.bed >> /galaxy/3.bed >> /galaxy/galaxy_symlink/test-data/4.bed >> /galaxy/galaxy_symlink/test-data/5.bed >> >> The Galaxy administrator may now safely delete /galaxy/import/link, >> but >> should >> take care not to remove the referenced symbolic links (/galaxy/3.bed, >> /galaxy/galaxy_symlink). >> >> Not all symbolic links are dereferenced because it is assumed that if >> an >> administrator links to a path in the import directory which itself is >> (or >> contains) links, that is the preferred path for accessing the data. >> >> >> >> Oliver Hofmann wrote: >>> Dear all, >>> >>> >>> to echo what Abhi said: we are also currently looking of ways to >>> automatically import data sets (libraries) into Galaxy without >>> having >>> to >>> manually trigger the import via the administration interface, and >>> ideally >>> while keeping the data in the original place. The idea here is to >>> have >>> multiple tools all point at the original 'source data' without >>> having >>> to >>> replicate terabytes of data. >>> >>> Not quite sure how feasible this is in practice, but it certainly >>> would >>> be >>> incredibly helpful. >>> >>> Best, >>> >>>    Oliver >>> >>> >>> >>> >>> On 28 Sep 2009, at 14:24, Abhishek Pratap wrote: >>> >>>> HI Greg >>>> >>>> Thanks for a quick reply and making some requested changes. However >>>> I >>>> am >>>> not still sure if importing NGS data will help in long run. >>>> >>>> For Centers generating NGS data which could 2-3 T.B / week >>>> depending >>>> on >>>> no. of sequencers I think importing another copy of raw data into >>>> galaxy >>>> workspace will be asking for lot of disk space. I understand it is >>>> a >>>> neat >>>> way of doing things as it becomes agnostic of the raw data location >>>>  but >>>> might not be the best way for handling huge data in long run for >>>> centers >>>> like ours. >>>> >>>> Please correct me if I am wrong. I think we could also have a >>>> simple >>>> option without having to import the data and just using it for >>>> analysis >>>> from >>>> the current location, also storing results at the same location. >>>> That >>>> way in >>>> future even if the data set is moved analysis also stays with it. >>>> >>>> Let me know what you feel. I will be happy to know if there are any >>>> other >>>> smart reasons of importing the data in galaxy workspace just for >>>> curiosity >>>> sake. >>>> >>>> Thanks, >>>> -Abhi >>>> >>>> On Mon, Sep 28, 2009 at 9:28 AM, Greg Von Kuster <ghv2@psu.edu> >>>> wrote: >>>> Hello Abhishek, >>>> >>>> The Galaxy distribution includes the enhancements to which I >>>> previously >>>> referred for uploading history files.  Uploading files >>>> to a >>>> history >>>> now >>>> creates a Galaxy job just like any other tool, and can be run on a >>>> cluster >>>> node, allowing upload of very large files.  The initial >>>> pass of >>>> this >>>> work is >>>> also completed for uploading to a Data Library, but this >>>> enhancement >>>> is >>>> still in test, so it should soon be available in the distribution. >>>> >>>> Do you want to avoid having to import at all (e.g. allow Galaxy to >>>> refer >>>> to datasets that live in their original locations)? >>>>  This is not >>>> currently >>>> possible, but if this is what you are looking for, we can consider >>>> some >>>> additional options on the current upload form, or possibly a new, >>>> separate >>>> form. >>>> >>>> >>>> Greg Von Kuster >>>> Galaxy Development Team >>>> >>>> >>>> Abhishek Pratap wrote: >>>> Hi Greg, Anton and all >>>> >>>> Just wondering if there has been any progress made on this end. I >>>> am >>>> sorry I was not able to follow it up on Assaf's suggestion due to >>>> other >>>> things at work. >>>> >>>> I did try the latest version of galaxy and looks like the files are >>>> still >>>> transferred over HTTP before they could be used in the galaxy >>>> workspace. >>>> Also I would again like to highlight that many labs might want to >>>> use >>>> the >>>> local instance of galaxy and prefer to point to a local path where >>>> the >>>> file >>>> is being stored. That way we will have both the benefits of using a >>>> cool GUI >>>> and process data stored locally. >>>> >>>> Let me know if you guys need some feedback or have more questions. >>>> I >>>> will >>>> be happy to discuss them. >>>> >>>> best, >>>> -Abhi >>>> >>>> On Tue, Jul 21, 2009 at 4:26 PM, Greg Von Kuster <ghv2@psu.edu >>>> <mailto:ghv2@psu.edu>> wrote: >>>> >>>>   Hello Abishek, >>>> >>>>   We are currently in the process of significantly >>>> enhancing the >>>>   current Galaxy upload utilities, and the new version >>>> should >>>>   eliminate the issue you've raised about the time >>>> needed to >>>> upload >>>>   large files via HTTP ( not for making an initial copy >>>> of the >>>> file in >>>>   the Galaxy environment ). However, it will probably >>>> not be >>>> ready for >>>>   release for a few more weeks, so if you can take >>>> advantage of >>>>   Assaf's script in the meantime, that's great. >>>> ¨ÜI can't >>>> guarantee >>>>   that all Galaxy features will function correctly if >>>> you do this >>>> though. >>>> >>>>   Assaf, have you found that using your script breaks >>>> anything? >>>> >>>>   Also, if you upload a file to a library rather than a >>>> history, >>>>   multiple users can "import" the library dataset into >>>> their >>>> history >>>>   for analysis, but there is only 1 file on disk ( users >>>> are >>>> pointing >>>>   to it from their histories ). ¨ÜBut >>>> uploading a file to >>>> a history >>>>   will create a new copy of the file each time it is >>>> uploaded. >>>> >>>>   Greg Von Kuster >>>>   Galaxy Development Team >>>> >>>> >>>> >>>>   Abhishek Pratap wrote: >>>> >>>>       Hi All >>>> >>>>       @Greg : Please find my >>>> comments below. >>>> >>>>       On Tue, Jul 21, 2009 at >>>> 10:44 AM, Greg Von >>>> Kuster<ghv2@psu.edu >>>>       <mailto:ghv2@psu.edu>> >>>> wrote: >>>> >>>>           >>>> Hello Abhi, >>>> >>>>           >>>> Can you clarify the steps you took that >>>> produced the >>>>           >>>> behavior? ǃÜSee my >>>> >>>>           >>>> comments below. >>>> >>>>           >>>> Anton Nekrutenko wrote: >>>> >>>>           >>>>     Abhishek: >>>> >>>>           >>>>     Let talk. This is the area >>>> of active current >>>>           >>>>     development. We are >>>> ǃÜlooking >>>> >>>>           >>>>     at implementing a universal >>>> fastq-like format or >>>>           >>>>     supporting >>>> ǃÜmultiple >>>> >>>>           >>>>     formats. Perhaps we should >>>> join efforts in ironing >>>> out >>>>           >>>>     >>>> ǃÜspecifications. >>>> >>>> >>>>           >>>>     anton >>>>           >>>>     galaxy team >>>> >>>> >>>>           >>>>     On Jul 20, 2009, at 5:18 >>>> PM, Abhishek Pratap >>>> wrote: >>>> >>>>           >>>>         Hi All >>>> >>>> >>>>           >>>>         I recently came >>>> to know about NGS analysis >>>> on galaxy >>>>           >>>>         during ISMB. >>>>           >>>>         Getting excited >>>> I tried couple of things >>>> basically >>>>           >>>>         to play with >>>> it. >>>> >>>>           >>>>         Few comments : >>>> I may have interepretted >>>> something >>>>           >>>>         described below >>>> in a >>>>           >>>>         wrong way. My >>>> apologies before hand. >>>> >>>> >>>> >>>>           >>>>         On a standalone >>>> installation of galaxy while >>>> I was >>>>           >>>>         trying to >>>> explore >>>>           >>>>         one >>>> FASTQ(sequence) file. It takes >>>> considerable (> >>>>           >>>>         20 min) for a >>>> fastq >>>>           >>>>         file to get >>>> uploaded (2 GB). >>>> >>>>           >>>> Are you using the Galaxy upload utility >>>> to create an >>>> item in >>>>           >>>> your history >>>>           >>>> that points to the dataset file on >>>> disk? >>>> >>>> >>>>       Yes that is precisely >>>> correct, I am trying to >>>> upload a solexa >>>> FASTQ >>>>       file but on a standalone >>>> galaxy installation from >>>> my local >>>> file >>>>       system. >>>> >>>>           I >>>> am not sure what is the rationale >>>> >>>>           >>>>         behind that. >>>> Ideally I think there should be >>>> no need >>>>           >>>>         to upload such >>>>           >>>>         heavy files >>>> into the workspace. >>>> >>>>           A >>>> data file that originates from a >>>> place external to >>>> Galaxy >>>>           >>>> must be uploaded >>>>           >>>> into Galaxy so that the disk file can >>>> be placed in the >>>>           >>>> location configured >>>>           in >>>> the Galaxy config file. >>>> ǃÜAlso, when data is >>>> uploaded to >>>> >>>>           >>>> Galaxy ( either >>>>           to >>>> a history or a library ), several >>>> database table >>>> settings >>>>           >>>> are created >>>>           >>>> that are used by various Galaxy >>>> features. >>>> >>>>           >>>> They could actually be used straight >>>> >>>> >>>>       Thanks for the clarification >>>> but I am not sure this >>>> will help >>>> a >>>>       lot of >>>>       people who are interested to >>>> install and run galaxy >>>> locally >>>>       mainly for >>>>       the following reasons. May >>>> be it is just local to >>>> me. >>>> >>>>       A. We already one instance >>>> of data saved on the >>>> local file >>>> system >>>>       B. Making another copy via >>>> galaxy will eat away a >>>> lot of space >>>>       in long run. >>>>       C. The time needed to import >>>> the files into galaxy >>>> space is >>>> huge >>>> >>>>           >>>>         away by the >>>> path specified. >>>> >>>>           >>>> What do you mean by "the path >>>> specified"? >>>> >>>> >>>> >>>>       Well what I mean was a way >>>> to specify the path of >>>> the file/run >>>>       on the >>>>       lcoal file system and galaxy >>>> could directly pick it >>>> up from >>>> there >>>>       rather than uploading it >>>> into its own space. Now I >>>> understand >>>> this >>>>       might not work based on the >>>> way the system was >>>> designed. >>>> >>>> >>>>           >>>> Also is there any way to access the >>>> >>>>           >>>>         scripts for >>>> analysis on the command line. I >>>> know >>>>           >>>>         this undermines >>>> the >>>>           >>>>         main aim of >>>> working with galaxy but rite now >>>> I am >>>>           >>>>         concerned about >>>> the >>>>           >>>>         >>>> performance/time. >>>> >>>>           >>>> You should be able to run any Galaxy >>>> tool from the >>>> command >>>>           >>>> line as long as >>>>           >>>> you have all of the tool's required >>>> binaries in your >>>> path. >>>>           >>>> ǃÜHowever, running >>>> >>>>           a >>>> tool from within Galaxy should >>>> generally not be any >>>> slower >>>>           >>>> than running it >>>>           >>>> outside of Galaxy, depending, of >>>> course, on what you are >>>> doing. >>>> >>>> >>>> >>>> >>>>       Ok I was under the >>>> impression that running from >>>> SHELL will >>>> eliminate >>>>       the step of uploading them >>>> into galaxy file space. >>>> >>>> >>>>       -Abhi >>>> >>>>           >>>>         I will be happy >>>> to discuss more about this >>>> in case >>>>           >>>>         you have some >>>>           >>>>         >>>> comments/questions for me. >>>> >>>> >>>> >>>>           >>>>         Best, >>>>           >>>>         -Abhi >>>> >>>> >>>> >>>>           >>>>         >>>> ----------------------------- >>>> >>>>           >>>>         Abhishek Pratap >>>> >>>>           >>>>         Bioinformatics >>>> Software Engineer >>>> >>>>           >>>>         Institute for >>>> Genome Sciences >>>> >>>>           >>>>         School of >>>> Medicine, Univ of Maryland >>>> >>>>           >>>>         801, W. >>>> Baltimore Street, Baltimore, MD >>>> 21209 >>>> >>>>           >>>>         Ph: >>>> (+1)-410-706-2296 >>>> >>>>           >>>>         >>>> www.igs.umaryland.edu/ >>>> <http://www.igs.umaryland.edu/> >>>>           >>>>         >>>> _______________________________________________ >>>>           >>>>         galaxy-user >>>> mailing list >>>>           >>>>         >>>> galaxy-user@bx.psu.edu >>>> <mailto:galaxy-user@bx.psu.edu> >>>> >>>> >>>> http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-user >>>> >>>>           >>>>     Anton Nekrutenko >>>>           >>>>     http://nekrut.bx.psu.edu >>>>           >>>>     http://galaxyproject.org >>>> >>>>           >>>>     >>>> _______________________________________________ >>>>           >>>>     galaxy-user mailing list >>>>           >>>>     galaxy-user@bx.psu.edu >>>> <mailto:galaxy-user@bx.psu.edu> >>>> >>>>           >>>>     >>>> http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-user >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> _______________________________________________ >>>> galaxy-user mailing list >>>> galaxy-user@bx.psu.edu >>>> http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-user >>> -- >>> Research Associate    Department of >>> Biostatistics >>> Associate Director    Bioinformatics Core >>>           >>>           >>>  Harvard School of Public Health >>> Skype: ohofmann       Phone: +1 >>> (617) 365 0984 >>> >>> >>>