Novice Questions

Question: Novice Questions

8.8 years ago by

Mariette • 30 wrote:

Hi, I'm currently using ergatis as workflow manager, and I'm looking at the differences between ergatis and galaxy. In order maybe to migrate to galaxy. One really important feature to me is the ability of ergatis to iterate against file liste. I haven't seen anything like this in galaxy, am I mistaking ? Other point there is a way to make galaxy using local files instead of importing all files on the server ? And finaly I was wondering if there is a way to configure galaxy, so the outputs are stored to the ldap-user home directory ? thanks for your reply, Jerome

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modified 7.4 years ago by Jeremy Goecks • 2.2k • written 8.8 years ago by Mariette • 30

8.8 years ago by

Hotz, Hans-Rudolf • 1.8k

Switzerland

Hotz, Hans-Rudolf • 1.8k wrote:

Jerome Well, I am tempting to say: 'everything' is possible with galaxy. Galaxy is so brilliant, because, you can easily modify the existing tools and you can add pretty much any tool you want (as long as it can be called from the command line). In our local Galaxy installation, we have added several tools which rely on files outside of the galaxy directory tree. Storing results in user home directories might be a little bit tricky, but I don't see major problems, as long as the server on which galaxy runs has access to the home directories, each home directory has a designated area with write permission for the 'user' galaxy and the individual users are logged in when they use galaxy....you will need to discuss this with your sysadmin. Once you have been using galaxy, you will probably realize, that you don't want to store results in home directories...especially if you work with large files (eg NGS). Take advantage of Galaxy, where every user has his/her own history (i.e. the datasets) on a central server. Enough "blabla" from my site - just download and install Galaxy. And you will soon realize its potential. Hans

ADD COMMENT • link written 8.8 years ago by Hotz, Hans-Rudolf • 1.8k

Hi Hans and Jerome, Although I do agree that Galaxy is a great tool :), one of the things Jerome asked is actually not possible: iterating over a list of files is currently a no go unless you want to click yourself into a sick leave due to RSI. This is something I would love to see as in some of our experiments we generate big collections of files. For example we use LC separation before MS usually generating something like 12 * 12 = 144. Manually uploading 144 files for processing in Galaxy is not fun. As a workaround we can sometimes merge the data from the fractions before uploading, but in that case you easily loose the link between the identified peptides and which fraction it was derived from, so this is suboptimal... So, more complex workflows with splitting, merging, looping, etc. are not (yet) possible with Galaxy as far as I know, but because Galaxy does not do this complex stuff, you don't need a manual to get started: KIS :). Cheers, Pi

ADD REPLY • link written 8.8 years ago by Pieter Neerincx • 360

7.4 years ago by

Jeremy Goecks • 2.2k

Jeremy Goecks • 2.2k wrote:

Hello Kurinji, Glad to hear that you found the workshop helpful. As a reminder, please email questions about using Galaxy and its tools to the galaxy- user mailing list (which I've cc'd). You may get quicker and different responses from community members, and everyone will benefit from the discussion. The best way to figure out which dataset corresponds with Cuffdiff's labels is to click the rerun button in the dataset: sample names correspond directly to the reads datasets (i.e. BAM files) provided as input to Cuffdiff. You'll need to use a reference annotation (GTF file) that has the gene_name attribute as input for Cufflinks/compare/difff. Typically Ensembl annotations have this attribute; however, you'll need to prepend 'chr' to each line--really, to each chromosome name--in order to bring Ensembl notation in line with UCSC/Galaxy notation. It's difficult for me to comment without seeing your analysis. Some output files depend on particular attributes being set correctly in the annotation file. You may want to search through our mailing list archives and see if your question has already been answered: http://gmod.827538.n3.nabble.com/Galaxy-Users-f815892.html Good luck, J.

ADD COMMENT • link written 7.4 years ago by Jeremy Goecks • 2.2k

Thanks for the reply. I tried to use the script provided on a previous galaxy thread for adding the chr on to the gtf file on the mac terminal but I keep getting this error - awk: can't open file ensembl.gtf source line number 1 I am very new to using the terminal so please let me know if there is something basic that I am not doing right, Thanks! Kurinji

ADD REPLY • link written 7.4 years ago by Kurinji Pandiyan • 10

7.4 years ago by

Jeremy Goecks • 2.2k

Jeremy Goecks • 2.2k wrote:

Try this Galaxy workflow: http://main.g2.bx.psu.edu/u/jeremy/w/make-ensembl-gtf-compatible-with- cufflinks It simply prepends 'chr' to the chromosome name, which is needed if you're using an Ensemble reference annotation and want to use it with Cufflinks/compare/diff in Galaxy. Best, J.

ADD COMMENT • link written 7.4 years ago by Jeremy Goecks • 2.2k

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