Re: [galaxy-user] Galaxy not showing my reference genome in Drop down for BowTie

pment list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://galaxyproject.org ___ The Galax

Re: [galaxy-user] from Galaxy to Megan

; in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/

Re: [galaxy-user] Error message on local install

all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: h

Re: [galaxy-user] job information on galaxy

nd other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://galaxyproject.org ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public serv

Re: [galaxy-user] Upload data to local Galaxy by copying them to the file folder

ist: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://galaxyproject.org ___ The Galaxy User list should be us

Re: [galaxy-user] "intersect" operation

your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://galaxyproject.org ___ The Galaxy User list should be used for the discussion of Galaxy analysis

Re: [galaxy-user] cuffdiff values different for same sample

e Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jack

Re: [galaxy-user] encode rna-seq data

Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson

Re: [galaxy-user] FW: problem in data uploading

use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://galaxyproject.org

Re: [galaxy-user] Error installing MACS on local Galaxy

axy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://galaxyproject.org ___

Re: [galaxy-user] The last column in the output file of 'Screen Motif'

listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://galaxyproject.org ___ The Galaxy User list should be used for the discussio

Re: [galaxy-user] cuffdiff values different for same sample

nstances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Ja

Re: [galaxy-user] Export to file

d the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://galaxyproject.org _

Re: [galaxy-user] cuffcompare input

evelopment list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://galaxyproject.org ___ The G

Re: [galaxy-user] Export to file

o import from file, the file needs to have a URL and I'm not sure how to go about that if the file is store locally on my computer. Thanks, Dave On Wed, Oct 17, 2012 at 6:12 PM, Jennifer Jackson mailto:j...@bx.psu.edu>> wrote: Hi Dave, To export larger files, you can use a d

Re: [galaxy-user] galaxy MAIN data problem

st by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use t

Re: [galaxy-user] Bowtie2 and Tophat2 for Galaxy

: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://galaxyproject.org ___ The Galaxy User list should be us

Re: [galaxy-user] using our own reference genome ?

cal Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ --

Re: [galaxy-user] More help neeeded

client. For discussion of > local Galaxy instances and the Galaxy source code, please > use the Galaxy Development list: > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > To manage your subscriptions to this and other Galaxy lists, > please use the interface at: >

[galaxy-user] help

ad . Please help me with this and i would be greatful if you could direct me to the right person who can help me sort this matter out . Thanking you Pranathi Pappu -- Jennifer Jackson http://galaxyproject.org ___ The Galaxy User l

Re: [galaxy-user] Fastq to Bam conversion on paired end reads picard

iscussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lis

Re: [galaxy-user] adding references

bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://galaxyproject.org ___ The Galaxy User list should be us

Re: [galaxy-user] Ion Torrent data analysis

http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://galaxyproject.org ___ The Galaxy User list should

Re: [galaxy-user] How to share a dataset without sharing my history ?

your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jenni

Re: [galaxy-user] MACS failed because of lambdaset options

ace at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://galaxyproject.org ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on t

Re: [galaxy-user] Latest supported Cufflinks?

urce code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson

Re: [galaxy-user] Latest supported Cufflinks?

appear to be unrelated to Cufflinks) Take care, Jen Galaxy team On 10/29/12 1:31 PM, Jennifer Jackson wrote: Hello Chris, Cufflinks 1.3 is currently supported. However, this may be unrelated, or rather you may need so solve another problem first. The error seems to be related to how you have

Re: [galaxy-user] primer contamination, miranalyzer

To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://galaxyproject.org ___ The Galaxy User list should be used for the discussion of Galaxy analy

[galaxy-user] Galaxy November 14, 2012 Distribution & News Brief

xes>, and several usability enhancements for *Datasets*, *Datatypes*, *Tools*, and *Tool Shed* functions. / http://getgalaxy.org/// /http://bitbucket.org/galaxy/galaxy-dist/ /http://galaxy-dist.readthedocs.org/ new: $ hg clone http://www.bx.psu.edu/hg/galaxy galax

Re: [galaxy-user] Map with Bowtie problem

your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://galaxyproject.org ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other

Re: [galaxy-user] Repeated Error with Tophat

lease use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://galaxyproject.org ___

Re: [galaxy-user] Help to identify variants with clinical/phenotype associations

e Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://galaxyproject.org _

Re: [galaxy-user] SNPeff on human genome

Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://galaxyproject.org ___

Re: [galaxy-user] Why is 'Filter pileup' not recegnising my 'Generate pileup' file?

http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://galaxyproject.org ___ The Galaxy User list sh

Re: [galaxy-user] BWA mapping with index file from history

code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://g

Re: [galaxy-user] Find out sense and antisense sequences

have employed 10 bp complementary criterion? For the antisense, the 5' will be T (in complementary to A). Besides, my library contains other small RNAs. That's why I concern output files of sense and antisense must have 10bp complementary. Another quick question, in you regular expre

Re: [galaxy-user] combining two fastq files

http://lists.bx.psu.edu/ -- Jennifer Jackson http://galaxyproject.org ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list

Re: [galaxy-user] combining two fastq files

ists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://galaxyproject.org ___ The Galaxy User list should be used fo

Re: [galaxy-user] History Pane empty?

.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://galaxyproject.org ___ The Galaxy User list should be used for the discussion

Re: [galaxy-user] Stitch Gene blocks return empty result???

sing "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at:

Re: [galaxy-user] Clip doesn't see my FASTQ file

to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://galaxyproject.org ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the pub

Re: [galaxy-user] filter for +/- 2-fold difference in expression levels

Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://galaxyproject.org ___ The Ga

Re: [galaxy-user] filter for +/- 2-fold difference in expression levels

*From:* Jennifer Jackson [j...@bx.psu.edu] *Sent:* Thursday, November 29, 2012 10:51 AM *To:* Ianiri, Giuseppe *Cc:* galaxy-user@lists.bx.psu.edu *Subject:* Re: [galaxy-user] filter for +/- 2-fold difference in expression levels Hello Giuseppe, Fold is

Re: [galaxy-user] Cuffdiff tracking file does not report all genes and trancrips from reference annotation?

anage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://galaxyproject.org ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other f

Re: [galaxy-user] History Pane empty?

listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://galaxyproject.org ___ The Galaxy User list should be used for the discussio

Re: [galaxy-user] dataset not visible

o this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://galaxyproject.org ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other featu

Re: [galaxy-user] extracting a subset of sequences from a very large fasta file(1.5 million)

uot;reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: htt

Re: [galaxy-user] how to download onto a server?

ource code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://galaxyproject.org __

Re: [galaxy-user] NGS with Arabidopsis thaliana built-in-index

iscussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson

[galaxy-user] December 3, 2012 Distribution & News Brief

.org/GalaxyUpdates/2012_12>*/. * http://getgalaxy.org* *http://bitbucket.org/galaxy/galaxy-dist* *http://galaxy-dist.readthedocs.org* new: $ hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist upgrade: $ hg pull -u -r f364d992270c * Thanks for using Galaxy!* The Gala

Re: [galaxy-user] Barcode splitting

For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://l

Re: [galaxy-user] NGS SAM Tools: Filter Pileup tool not working

all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.

Re: [galaxy-user] order of steps

y using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at

Re: [galaxy-user] Compute sum per row

Joachim Jacob wrote: Hi all, I wonder if there is a method for calculating a metric (e.g. sum) per row (working on a tabular dataset). But, each row contains a different number of values (i.e. some columns are empty). Can I compute this, using Compute?

Re: [galaxy-user] Tophat error.

discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http

Re: [galaxy-user] Windows function not working

ns to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://galaxyproject.org ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on t

Re: [galaxy-user] Sliding window to get average of a seq reads

y-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://galaxyproject.org ___ The Galaxy User list should be used for the discussion of Galax

Re: [galaxy-user] [galaxy-dev] How to add to add hg16 index into the build-in index / reference gnome list?

t: http://lists.bx.psu.edu/ -- Jennifer Jackson http://galaxyproject.org ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the lis

Re: [galaxy-user] Link to display BED files in UCSC Genome Browser

discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http

Re: [galaxy-user] Should fastq files be merged?

o this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://galaxyproject.org ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the pub

[galaxy-user] rice reference genome

n you direct me to the version of the genome used in Galaxy (oryza_sativa_japonica_nipponbare_IRGSP4.0)? Thanks! Aaron <http://www.smith.biology.lsu.edu/lab> -- Jennifer Jackson http://galaxyproject.org ___ The Galaxy User lis

Re: [galaxy-user] Data library and symbolic link

lic links because my data are frequently updated. The problem is that Galaxy takes the real link ("external_filename" column in "dataset" table) and doesn't find the files. Is there a way for galaxy to take the symbolic link in the database. Thanks in advance for y

Re: [galaxy-user] Bowtie index in data libraries

sion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Ja

[galaxy-user] rice reference genome

h.D. Assistant Professor Biological Sciences Louisiana State University 202 Life Sciences Building Baton Rouge, LA 70803 apsm...@lsu.edu <mailto:apsm...@lsu.edu> http://www.smith.biology.lsu.edu/lab *From:*Jennifer Jackson [mailto:j...@bx.psu.edu] *Sent:* Thursday, December 13, 2012 11:

Re: [galaxy-user] Galaxy Question

dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://galaxyproject.org ___ The Galaxy User list should be used for the discussion of Galaxy analysis a

Re: [galaxy-user] Galaxy Question

resulting job is green but empty and says "no peek" in the columns when I go to view. Do you know what this means? Thank you, Dominique On Mon, Dec 17, 2012 at 7:57 AM, Jennifer Jackson <mailto:j...@bx.psu.edu>> wrote: Hello Dominique, Would the tool 'NGS: QC a

Re: [galaxy-user] cufflinks analysis using .bam files generated by LifeScope (ABI 5500 Sequencer)

xy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http

Re: [galaxy-user] cufflinks analysis using .bam files generated by LifeScope (ABI 5500 Sequencer)

+33 4 72738322 150, cours Albert Thomas 69372 Lyon Cedex 08 France ---- *From:* Jennifer Jackson [j...@bx.psu.edu] *Sent:* Tuesday, December 18, 2012 2:53 AM *To:* Davide Degli Esposti *Cc:* galaxy-user@lists.bx.psu.edu *Subjec

Re: [galaxy-user] How to Provide .gtf file to tophat2

ist by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface

Re: [galaxy-user] add publicly available genomes?

8/12 12:40 PM, Camilla Nesbo wrote: Heia, Would it be possible to add the genome of Kosmotoga olearia (NC_012785) and Mesotoga prima (NC_017934) to the genomes availabe in galaxy database? Thanks, Camilla -- Jennifer Jackson http://galaxyp

[galaxy-user] Galaxy December 20, 2012 Distribution & News Brief

.edu/hg/galaxy galaxy-dist upgrade: $ hg pull -u -r 36ad8aa7b922 *Best wishes for a safe and happy holiday*, /*The Galaxy Team <http://wiki.galaxyproject.org/Galaxy%20Team>*/ -- Jennifer Jackson http://galaxyproject.org ___ The Galaxy User list should be

Re: [galaxy-user] How to display data at UCSC main?

ists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://galaxyproject.org ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. P

Re: [galaxy-user] Pipeline design for bacterial RNA-Seq

xy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://galaxyproject.org ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usega

Re: [galaxy-user] incompatible frame

.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://galaxyproject.org ___ The Galaxy User list should be used for

Re: [galaxy-user] BWA and FASTQ Joiner issues

Hi Hilde, Glad you wrote - we can try to help - On 1/10/13 8:33 AM, Hilde Stawski wrote: Hello, I hope someone might be able to help me with these issues, as I'm relatively new at Bioinformatics. When analyzing data on the main website of Galaxy (all samples from the same Illumina MiSeq ru

[galaxy-user] where to submit galaxy error messgae

Hi Kathryn, If you encounter an error while using the public Main Galaxy server at http://main.g2.bx.psu.edu (usegalaxy.org), the first thing to do is review the tool usage help (on tool form) and the input dataset formats. Often the error message or 'i' info page's standard out/error will have

Re: [galaxy-user] macs error for chipseq data

Hello Kathryn, This is occurring on your local Galaxy install? Have you installed the actual MACS tool and set up the proper configuration paths? Details for how to do this are in these wikis: http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies http://wiki.galaxyproject.org/Admin/To

[galaxy-user] Galaxy January 11, 2013 Distribution & News Brief

*Galaxy January 11, 2013 Distribution & News Brief* * Complete News Brief * * Highlights:* * /*GCC2013 Training Day Topic Nomination closes TODAY!*/ Read more...

[galaxy-user] Login problems

Myself and a co-worker are both having issues with uploading files on to our galaxy accounts through the FTP server. We can get our files transferred onto the FTP, but when we click "Get Data" and checkmark them to be loaded on the account, they sit indefinitely in the work queue. Both of us

Re: [galaxy-user] Problem with BWA?

Hi Mike, The public Main Galaxy instance has been very busy for the last week or so, and wait times for NGS jobs have been a bit longer than usual. The important part is to leave jobs in the waiting-to-run "grey" state and not stop/restart or they will effectively be moved back to the end of

Re: [galaxy-user] long waiting time for Bowtie jobs?

Hi Suzie, The main Public Galaxy server has been very busy this last week and jobs have been waiting in queue for a bit longer than normal. You jobs should have completed for now, but for next time or for other readers - the best strategy when the queue is busy is to start the most important

Re: [galaxy-user] Problem Joining Two Datasets

Hello Kim, We can confirm that a few of the newest datasets in your most recent history have odd properties. The way around this is to copy the datasets into a new history (an option under "History" menu), convert the delimiters to tabs (a tool under "Text Manipulation"), then use the join to

Re: [galaxy-user] reference annotation for whole transcriptome RNA-Seq

Hi Davide, Yes, if the iGenomes annotation data collection includes a reference GTF dataset for your genome, that would be the best choice, as it would include all of the attributes that the RNA-seq tools (Cufflinks, CuffDiff, etc) require for full functionality. The hg19 and mm9 GTF files ar

Re: [galaxy-user] How to determine differentially expressed genes using Galaxy?

Hello, There are many ways to use Galaxy, and the tools offered/available in each is often a choice made by the group hosting the instance (not the version of the underlying code base): http://wiki.galaxyproject.org/Big%20Picture/Choices Wrappers for this tool are available from the tool shed

Re: [galaxy-user] Mapping miRNA data

Hello Mark, The public Main Galaxy instance has been very busy for the last week or so. The best strategy is to start the jobs that are the most important first, to leave these queued, and to not stop/restart jobs. These will eventually run in the order they were submitted with respect to othe

Re: [galaxy-user] can't download big files

Hi Allan, It should be possible to just use the save function (disc icon) to download datasets of this size to your local computer. As for curl, this also is an alternative. If it not functioning, you might want to try to see if it will function on other files (not part of Galaxy), just to te

Re: [galaxy-user] running time of Cufflinks on main Galaxy

Hi Davide, The public Main Galaxy server has been quite busy the last week or so. But it is actually a bit less busy at this time comparatively, so you may have noticed your jobs moving along. The most effective strategy when using the public resource is to queue your jobs then leave them in

Re: [galaxy-user] error message running Cufflinks on local galaxy

Hi Davide, Is this the same job as you can on the public Galaxy Main instance (same inputs/settings)? If so, let's review that one once the bug report comes in and see if the there is a data issue we can trace back to as one of the first steps (GTF file or other). Jeremy might also have more

Re: [galaxy-user] error running cufflinks

Hi Davide, Would you be able to send this in as a bug report? This will allow us to check out the details. You basically just click on the "green bug icon" for one of the datasets in the group and submit, but this wiki also explains: http://wiki.galaxyproject.org/Support#Reporting_tool_errors

Re: [galaxy-user] Galaxy Help

Hi John, The current link is: http://wiki.galaxyproject.org/FTPUpload We changed our wiki base and many of the older links do not redirect. I'll let our wiki admin Dave know about this and see what can be done. If this comes up again soon, the base always redirects to "http://galaxyproject.o

Re: [galaxy-user] Galaxy Help

nce alignments. Thank you, -John On Sun, Feb 3, 2013 at 1:34 PM, Jennifer Jackson mailto:j...@bx.psu.edu>> wrote: Hi John, The current link is: http://wiki.galaxyproject.org/__FTPUpload <http://wiki.galaxyproject.org/FTPUpload> We changed our wiki base and many o

Re: [galaxy-user] Problems with large gzipped fasta files

Hi Jim, You message was misthreaded (perhaps a reply to another thread, with just the subject line changed?), but I was able to dig it out. A this time, there are no known issues with FTP Upload to the public Main server. Any issues you have have found prior were either related to a problem

[galaxy-user] Galaxy February 8, 2013 Distribution & News Brief

Galaxy Feb 8, 2013 Distribution & News Brief *Complete News Brief * *Highlights:* * /Improvements/ to our release process

Re: [galaxy-user] Galaxy Join takes too long?

Hello Milad, I am not sure if you are using the public Galaxy Main server (https://main.g2.bx.psu.edu) or your own local computer, or if the jobs are yellow and running or still grey and in the waiting-to-run stage. If using Galaxy Main, and if actually running (dataset is yellow), this type

Re: [galaxy-user] Reference Genome in Lastz

Hello, The quickest way to use a new, small genome such as this one is use it as a custom reference genome with the tool. Instructions are here: http://wiki.galaxyproject.org/Support#Custom_reference_genome Best, Jen Galaxy team On 2/13/13 7:18 AM, Murphy, Caitlin N wrote: I'm trying to map a

Re: [galaxy-user] Problem

Hello Christopher, The reference annotation will need to include the attribute gene_name in order for this to be in the final output. If not provided, gene_id from the GTF/GFF3 file will be in the output instead. In addition, if the reference annotation does not contain the attributes p_id and

Re: [galaxy-user] galaxy-user submission

Hello Oya, This wiki has links to where you can add yourself to the list. http://wiki.galaxyproject.org/MailingLists#Subscribing_and_Unsubscribing Other general info about mailing lists: http://wiki.galaxyproject.org/Support#Mailing_Lists Best, Jen Galaxy team On 2/13/13 11:07 PM, Oya Uygune

Re: [galaxy-user] Uploading large archive histories

Hi Getiria, Jeremy gave advice for the local, but I wanted to follow up about the trouble you were having uploading to the public Main Galaxy instance at https://main.g2.bx.psu.edu/ (usegalaxy.org). Would you please try a larger history upload again today, if you have not already done so, and

Re: [galaxy-user] mitochondrial transcripts

Hello Tim, The problem is either that the reference genome build used does not contain the mitochondrial genome sequence, that the reference annotation file that you are using with the Cufflinks does not include mitochondrial annotation, or that the identifiers between the reference genome an

Re: [galaxy-user] mitochondrial transcripts

same mm10 reference genome with Cufflinks. Since I didn't use a custom genome, it seems as though there should not be any identifier mismatchesŠ(?) Tim On 2/19/13 1:54 PM, "Jennifer Jackson" wrote: Hello Tim, The problem is either that the reference genome build used does

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