Re: [galaxy-user] [Ticket#2013010710000031] Installation de ChipMunk sur Genotoul

Thanks Alban for your answer, Our admin system has tested to run ChIPMunk externally but didn't received the same error message. In fact, pretty.rb lib is found. It seems to be a difference between chiphorde version : we have run_chiphorde4.rb instead of run_chiphorde.rb Do you think that

Re: [galaxy-user] [Ticket#2013010710000031] Installation de ChipMunk sur Genotoul

Thanks to Marie-Stephane to have found that this error is due to a diifference of verion. Alban, could you please tell us which version (2 or 3) do you use in your Galaxy tools, in order to install this version on our cluster ? Thanks in advance, Sarah Sarah Maman a écrit : Thanks Alban for

[galaxy-user] Download data using FTP-access?

Is there any way of downloading processed files at galaxyproject.org by e.g. FTP, instead of “Save as” in the web browser? I have some large (~50Gb) BAM files to download, and downloading it via the browser is not stable. Thanks, Karen.

Re: [galaxy-user] Trackster custom builds wrong

Hello, Can you share with me (a) the fasta dataset and (b) the form values (e.g. name, dbkey, etc) you used when you encountered this error? Thanks, J. On Jan 7, 2013, at 10:17 AM, Jennifer Hillman-Jackson wrote: Repost to Galaxy-user --- When using Trackster on Galaxy(

Re: [galaxy-user] nebula suite / _chiphorde.log not found

Hi Sarah, It seems that Chipmunk is not well executed (reason why it can't found the log file). I think that there's some ruby libraries missing. Please try to run ChIPMunk externally this way: ruby /path/to/ChIPMunk/run_chiphorde.rb If you receive this kind of error message, it means that

Re: [galaxy-user] [Ticket#2013010710000031] Installation de ChipMunk sur Genotoul

Hi, You have to use ChIPMunk v2 with Nebula (I don't think its compatible with the v3) ++, Alban -- Alban Lermine Unité 900: INSERM - Mines ParisTech - Institut Curie Bioinformatics and Computational Systems Biology of Cancer 11-13 rue Pierre et Marie Curie (1er étage) - 75005 Paris - France

Re: [galaxy-user] identify different number of differential expressed genes using ensemble or reseq GTF

Hi, Another approach you can try is to use DESeq or EdgeR from Bioconductor to assess differential expression. I personally like these two methods LOTS better than Cuff* mainly because they are a lot closer to tried and true statistical methods developed for microarrays. I esp. like how both

Re: [galaxy-user] Download data using FTP-access?

Hello Karen, From a shell/unix/terminal window on your side, use curl to download datasets. The link can be obtained by right clicking the floppy disk icon inside a history item and choosing Copy Link Address (for most datasets) or Download Dataset/Download bam_index (for BAM datasets

[galaxy-user] Search software on public Galaxy servers

Hi community, Due to the increasing Galaxy public servers PublicGalaxyServershttp://wiki.galaxyproject.org/PublicGalaxyServers it would be very useful to have a search tool in order to look for software ready-to-use in the public servers. Since I know this is not available. Will it be feasible?

Re: [galaxy-user] Remove unpaired reads from quality-filtered pared-end fastq files.

Not the most convenient solution, but what I normally do in this situation is to combine the two files, filter then split again. There are tools for combining and splitting paired fastq files in Galaxy. Hope it helps, Carlos On Jan 8, 2013 12:55 AM, 柴田 弘紀 hshib...@gen.kyushu-u.ac.jp wrote: Hi

[galaxy-user] Fwd: joining two FASTq files with overlap reads

Sorry to send you again and look forward any input abut joining two overlapping reads Fastq files Thanks Kanwar -- Forwarded message -- From: shamsher jagaut kanwar...@gmail.com Date: Sun, Jan 6, 2013 at 2:24 PM Subject: joining two FASTq files with overlap reads To: galaxy-user