January 2014 - galaxy-dev - lists.galaxyproject.org

how to stop extra html file inserted into download zip
by Neil.Burdett＠csiro.au 10 Jan '14

10 Jan '14

Hi, I have a tool that works well. However, when I download the results, the results are zipped up but included into the zip file is the *.html file (with the same name as the tool output) do you know how I can stop this from being zipped up? Thanks Neil

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repository metadata reset not always working
by Lukasse, Pieter 09 Jan '14

09 Jan '14

Hi Greg, I found an issue in Toolshed, not sure if it has been reported before. Steps: 1- Make a repository and add a tool .xml and a README file 2- Reset metadata and check if all information appears in the toolshed UI 3- Now delete the README file from the hg repository 4- Commit 5- (not sure whether I did this step) reset metadata 6- Now add the README file back but with different contents. Commit, reset metadata 7- In the toolshed UI you will see that the OLD REAME contents are displayed. This is just one example...I have the feeling it is not restricted to the README files of course...so it can be quite a serious issue. Regards, Pieter Lukasse Wageningen UR, Plant Research International Departments of Bioscience and Bioinformatics Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands +31-317481122; skype: pieter.lukasse.wur http://www.pri.wur.nl<http://www.pri.wur.nl/>

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workflow small RNA sequencing Ion Proton platform
by Ilse van de Vondervoort 09 Jan '14

09 Jan '14

Dear developers, Very recently, I got introduced to Galaxy during a course. Now I am trying to analyse my own microRNA sequencing data (platform Ion Proton). However, all tools I wanted to use so far are either for Illumina or SOLiD platforms. Which tools, relevant for microRNA sequencing, can I use with FASTQ data from Ion Proton runs? Additionally, I can’t find any workflows for small RNA sequencing on the Galaxy wiki. Is there anybody that has experience with this? Thank you in advance. Kind regards, Ilse van de Vondervoort

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Bowtie: reference genome not listed
by Ilse van de Vondervoort 09 Jan '14

09 Jan '14

Dear developers, I encountered a problem when I wanted to map rat microRNA sequencing data (FASTQ file, after FASTQ Groomer) to the reference genome (see attached screenshot). I am unable to select any build-in reference genome, and I haven’t used any myself thus I can’t select one from my history. Hopefully, this is an easy to overcome issue. Kind regards, Ilse

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Continued issue fetching eggs
by Iry Witham 07 Jan '14

07 Jan '14

Hi Team, Quite some time back I posted that I was unable to upgrade my local galaxy instance due to issues fetching eggs. I have not been able to get this resolved and was wondering if I could get some help. The error I get is: python scripts/fetch_eggs.py Warning: setuptools (a dependent egg of sqlalchemy-migrate) cannot be fetched Thanks, Iry The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.

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GCC2014 Training Day Topic Voting open January 6-17
by Dave Clements 06 Jan '14

06 Jan '14

Hello all, What topics should be offered at the GCC2014 Training Day<https://wiki.galaxyproject.org/Events/GCC2014/TrainingDay> ? Topics <https://wiki.galaxyproject.org/Events/GCC2014/TrainingDay> for the GCC2014 Training Day <https://wiki.galaxyproject.org/Events/GCC2014/TrainingDay> are selected by you, the Galaxy Community. For GCC2014 there are 19 nominated topics<https://wiki.galaxyproject.org/Events/GCC2014/TrainingDay#Nominated_Topics> to pick from. Your votes will determine the topics that are offered, which topics should be offered more than once, and which ones should not be scheduled at the same time. Your vote matters. *Topic voting closes January 17.* The Training Day schedule, including instructors, will be published before early registration opens on February 10. Vote now! <https://wiki.galaxyproject.org/Events/GCC2014/TrainingDay> *About the GCC2014 Training Day <https://wiki.galaxyproject.org/Events/GCC2014/TrainingDay>:* The 2014 Galaxy Community Conference (GCC2014)<https://wiki.galaxyproject.org/Events/GCC2014> will start on June 30 with a Training Day<https://wiki.galaxyproject.org/Events/GCC2014/TrainingDay> featuring 4 parallel tracks, each with three workshops, each of which are two and a half hours long, for a total of twelve sessions. There will be at least one complete track (3 consecutive workshops) about using Galaxy for biological research, and at least one full track on deploying and managing Galaxy instances. As always, please let us know if you have any questions. Thanks, The GCC2014 Organizing Committee<https://wiki.galaxyproject.org/Events/GCC2014/Organizers> -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/

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Cloud Launch - Where is /mnt/galaxyData
by greg 06 Jan '14

06 Jan '14

Hi guys, I just launched an instance from https://usegalaxy.org/cloudlaunch and chose "data cluster" when prompted. Everything seems to have gone ok, but when I ssh in, I don't see /mnt/galaxyData Background: Basically we have a bioinformatics tool that needs SGE to run. So I want to install it on a galaxy cloud instance and then provide the share string to other researchers. I did this successfully a year or two ago by installing it to /mnt/galaxyData. Thanks, Greg

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Re: [galaxy-dev] faToTwoBit: not found / trackster
by Jasper Koehorst 06 Jan '14

06 Jan '14

Yes and i even chmodded it to 777 for testing purposes. When I run it I get the option overview of the tool. I can't copy that right now (out of office) but the application works as I also 2bitted a genome. > On 04 Jan 2014, at 18:37, Jeremy Goecks <jeremy.goecks(a)emory.edu> wrote: > > Can you run the faToTwoBit tool from the command line? It can be difficult to find the right executable for UCSC tools sometimes; if you have the wrong executable (e.g. 32 bit instead of 64 bit), you'll see the misleading 'not found' error. > > Best, > J. > > On Jan 3, 2014, at 11:35 AM, Jasper Jan Koehorst <jasper.koehorst(a)wur.nl<mailto:jasper.koehorst@wur.nl>> wrote: > > > First of all, best wishes! > > I was/am trying to visualize a GTF file in galaxy on a local 64 bit ubuntu system. However I stumbled upon an issue were it remained grey. When I did an automaic visualization I saw a line that went up and down over the chromosome. When I switched to pack I got a grey / / / line slashed output. > > I contacted dannon and ceberhard on IRC and they told me to add a print statement on line 200 for the tracker. This visualized the following error: > > {'kind': 'error', 'message': '/bin/sh: 1: faToTwoBit: not found\n'} > > So I downloaded and placed the faToTwoBit file in /usr/bin I even chmodded it to 777 but the error remained. I also started digging into the code on where it calls the application and added /usr/bin/ in front of it but no luck so far. > > Anyone has a clue on what is happening? It almost must be an ubuntu related issue as I dont see how galaxy cannot find the path. > > $PATH is still properly set when running galaxy as I added echo $path it to a tool and it returned > > /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/bin > > The IRC chat can be seen here: > > http://pastebin.com/9fZrkRDn > > Thanks a lot, > > > /home/galaxy/HB27.2bit10.64.9.118 - - [03/Jan/2014:17:24:34 +0200] "GET /api/datasets/e2132aef71b11dbf?data_type=data&chrom=chr&low=0&high=320487&mode=Auto&resolution=801.216067653277&hda_ldda=hda&filter_cols=%5B%22Score%22%5D HTTP/1.1" 200 - "http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbf&hda_ld…" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36" > > 10.64.9.118 - - [03/Jan/2014:17:24:34 +0200] "GET /api/datasets/e2132aef71b11dbf?data_type=data&chrom=chr&low=1602432&high=1894876&mode=Auto&resolution=801.216067653277&hda_ldda=hda&filter_cols=%5B%22Score%22%5D HTTP/1.1" 200 - "http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbf&hda_ld…" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36" > > 10.64.9.118 - - [03/Jan/2014:17:24:34 +0200] "GET /api/datasets/e2132aef71b11dbf?data_type=data&chrom=chr&low=1281945&high=1602432&mode=Auto&resolution=801.216067653277&hda_ldda=hda&filter_cols=%5B%22Score%22%5D HTTP/1.1" 200 - "http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbf&hda_ld…" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36" > > 10.64.9.118 - - [03/Jan/2014:17:24:34 +0200] "GET /api/datasets/e2132aef71b11dbf?data_type=data&chrom=chr&low=320486&high=640973&mode=Auto&resolution=801.216067653277&hda_ldda=hda&filter_cols=%5B%22Score%22%5D HTTP/1.1" 200 - "http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbf&hda_ld…" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36" > > 10.64.9.118 - - [03/Jan/2014:17:24:34 +0200] "GET /api/datasets/e2132aef71b11dbf?data_type=data&chrom=chr&low=961459&high=1281946&mode=Auto&resolution=801.216067653277&hda_ldda=hda&filter_cols=%5B%22Score%22%5D HTTP/1.1" 200 - "http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbf&hda_ld…" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36" > > 10.64.9.118 - - [03/Jan/2014:17:24:34 +0200] "GET /api/datasets/e2132aef71b11dbf?data_type=data&chrom=chr&low=640972&high=961459&mode=Auto&resolution=801.216067653277&hda_ldda=hda&filter_cols=%5B%22Score%22%5D HTTP/1.1" 200 - "http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbf&hda_ld…" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36" > > {'kind': 'error', 'message': '/bin/sh: 1: faToTwoBit: not found\n'} > > galaxy.webapps.galaxy.api.datasets ERROR 2014-01-03 17:24:36,418 Error in dataset API at listing contents: 'data': 'data' > > Traceback (most recent call last): > > File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", line 46, in show > > rval = self._data( trans, dataset, **kwd ) > > File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", line 201, in _data > > ref_seq = data_dict[ 'data' ] > > KeyError: 'data' > > 10.64.9.118 - - [03/Jan/2014:17:24:35 +0200] "GET /api/datasets/e2132aef71b11dbf?data_type=data&chrom=chr&low=320486&high=640973&mode=Pack&resolution=801.216067653277&hda_ldda=hda&filter_cols=%5B%22Score%22%5D HTTP/1.1" 500 - "http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbf&hda_ld…" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36" > > {'kind': 'error', 'message': '/bin/sh: 1: faToTwoBit: not found\n'} > > galaxy.webapps.galaxy.api.datasets ERROR 2014-01-03 17:24:36,595 Error in dataset API at listing contents: 'data': 'data' > > Traceback (most recent call last): > > File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", line 46, in show > > rval = self._data( trans, dataset, **kwd ) > > File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", line 201, in _data > > ref_seq = data_dict[ 'data' ] > > KeyError: 'data' > > 10.64.9.118 - - [03/Jan/2014:17:24:35 +0200] "GET /api/datasets/e2132aef71b11dbf?data_type=data&chrom=chr&low=0&high=320487&mode=Pack&resolution=801.216067653277&hda_ldda=hda&filter_cols=%5B%22Score%22%5D HTTP/1.1" 500 - "http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbf&hda_ld…" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36" > > {'kind': 'error', 'message': '/bin/sh: 1: faToTwoBit: not found\n'} > > {'kind': 'error'galaxy.webapps.galaxy.api.datasets ERROR 2014-01-03 17:24:37,049 Error in dataset API at listing contents: 'data': 'data' > > Traceback (most recent call last): > > File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", line 46, in show > > rval = self._data( trans, dataset, **kwd ) > > File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", line 201, in _data > > ref_seq = data_dict[ 'data' ] > > KeyError: 'data' > > , 'message': '/bin/sh: 1: faToTwoBit: not found\n'} > > 10.64.9.118 - - [03/Jan/2014:17:24:35 +0200] "GET /api/datasets/e2132aef71b11dbf?data_type=data&chrom=chr&low=1602432&high=1894876&mode=Pack&resolution=801.216067653277&hda_ldda=hda&filter_cols=%5B%22Score%22%5D HTTP/1.1" 500 - "http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbf&hda_ld…" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36" > > {{'kind': 'error', 'message''kind'galaxy.webapps.galaxy.api.datasets ERROR 2014-01-03 17:24:37,099 Error in dataset API at listing contents: 'data': 'data' > > Traceback (most recent call last): > > File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", line 46, in show > > rval = self._data( trans, dataset, **kwd ) > > File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", line 201, in _data > > ref_seq = data_dict[ 'data' ] > > KeyError: 'data' > > : : 'error'10.64.9.118 - - [03/Jan/2014:17:24:35 +0200] "GET /api/datasets/e2132aef71b11dbf?data_type=data&chrom=chr&low=961459&high=1281946&mode=Pack&resolution=801.216067653277&hda_ldda=hda&filter_cols=%5B%22Score%22%5D HTTP/1.1" 500 - "http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbf&hda_ld…" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36" > > '/bin/sh: 1: faToTwoBit: not found\n', 'message': '/bin/sh: 1: faToTwoBit: not found\n'} > > } > > galaxy.webapps.galaxy.api.datasets ERROR 2014-01-03 17:24:37,102 Error in dataset API at listing contents: 'data': 'data' > > Traceback (most recent call last): > > File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", line 46, in show > > rval = self._data( trans, dataset, **kwd ) > > File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", line 201, in _data > > ref_seq = data_dict[ 'data' ] > > KeyError: 'data' > > 10.64.9.118 - - [03/Jan/2014:17:24:35 +0200] "GET /api/datasets/e2132aef71b11dbf?data_type=data&chrom=chr&low=640972&high=961459&mode=Pack&resolution=801.216067653277&hda_ldda=hda&filter_cols=%5B%22Score%22%5D HTTP/1.1" 500 - "http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbf&hda_ld…" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36" > > galaxy.webapps.galaxy.api.datasets ERROR 2014-01-03 17:24:37,102 Error in dataset API at listing contents: 'data': 'data' > > Traceback (most recent call last): > > File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", line 46, in show > > rval = self._data( trans, dataset, **kwd ) > > File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", line 201, in _data > > ref_seq = data_dict[ 'data' ] > > KeyError: 'data' > > 10.64.9.118 - - [03/Jan/2014:17:24:35 +0200] "GET /api/datasets/e2132aef71b11dbf?data_type=data&chrom=chr&low=1281945&high=1602432&mode=Pack&resolution=801.216067653277&hda_ldda=hda&filter_cols=%5B%22Score%22%5D HTTP/1.1" 500 - "http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbf&hda_ld…" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36" > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ > >

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Small icon bug in local galaxy install
by Dooley, Damion 06 Jan '14

06 Jan '14

A few of our local galaxy installs have a relative folder path (i.e. in universe_wsgi.ini, "prefix = /galaxylab") . In the Admin tab, "Manage installed tool shed repositories", the icons in the legend below aren't showing because they have an absolute url: <img src="/static/june_2007_style/blue/ok_small.png" /> I can see in the galaxy-central/lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py code: return '<img src="/static/june_2007_style/blue/ok_small.png" %s/>' % latest_revision_tip_str Our /galaxylab is on galaxy changeset: 11247:a9a0ac9c1afa So I presume this code should be enhanced to get the prefix in there, or made a relative url? Regards, Damion

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Re: [galaxy-dev] Help Needed
by Jennifer Jackson 05 Jan '14

05 Jan '14

Hello Elsayed, Your protocol below seems to be a mix of a variant detection and an RNA-seq workflow. To build a workflow for RNA-seq, you will want to compare your steps with the protocols in the link that I sent you. If you want more examples, many more can be found here (for both RNA-seq and variant analysis, these are distinct analysis). Some have workflows that you can import and use directly or modify. https://wiki.galaxyproject.org/Learn#Other_Tutorials Shared Data -> Published Pages In particular, there is a sample workflow in this tutorial that will help you to understand what the different steps are for and what order they go in. https://usegalaxy.org/u/jeremy/p/galaxy-rna-seq-analysis-exercise Best, Jen Galaxy team On 1/3/14 10:57 AM, Elsayed Hejazy wrote: > *Dear Dr. Jennifer,* > A lot of thanks for your reply its really mean alot for me. > i am still NGS junior i trying to do the following steps kindly give > me the right order for these procedures > Data Description: i have to samples each sample consists of 14 FASTQ > file (7 forward and 7 reverse ) i think this mean its paired end from > Illumina then i will try the following workflow to got best results > 1- Drag tow input dataset into workflow one for forward sequences file > and one for reverse to use paired end option in TOPHAT tool later and > when i run this workflow i will select multiple selection for the 7 > forward files to analyse all of them at the same time > 2- Drag FASTQC and link with last step for each to got if these file > may be illmina 1.8 version or older. > 3- Drag FASTQ Groomer and link with last step if files older than 1.8 > version to prepare as .FASTQSANGER format. > 4- Drag Filter FASTQ and link with last step to remove redundancy of > sequences. > 5- Drag FASTQ trimmer to remove unwanted ends of sequenced may occur > 6- Drag Manipulate FASTQ and link with last step (i dont know why). > the above six steps done twice to generate to files as output to make > as input for the following steps. > 7- Drag TOPHAT for illumina and make it accept paired end files and > link each file generated from QC to TOPHAT this step used to align and > map with reference genome. > 8- Drag Cufflinks and link with aligned BAM file generated from TOPHAT > to create an assembly > 9- Drag Cuffmerge and link with GTF file from Cufflinks this step to > merge all assemblies generated in Cufflinks > 10- Drag Cuffcompare and link with last step to got detailed reports > for accuracy of all generated assemblies. > 11- Drag MPileup and link with TOPHAT BAM file to generate file > containing SNPs sites. > 12- Drag Pileup-to-Interval and link with MPileup step to filter the > number of output SNPs to successive one or the most accurate. (i dont > know what is the difference between this tool and Filter Pileup). > - i dont know what is the tools used to know the copy number variation > CNV > i need to know how to separate human sequences from sample may > infected with any other sequences (is this at alignment stage) > i need to know the perfect order of steps if this order is not > completely right. > > Is this what i should do to make a good NGS workflow got all possible > information form dataset > > Really i am so so so sorry for disturbance - waiting your reply > Best Regards, > elsayed > > > > On Thu, Jan 2, 2014 at 6:05 PM, Jennifer Jackson <jen(a)bx.psu.edu > <mailto:jen@bx.psu.edu>> wrote: > > Hello Elsayed, > > Protocol help for RNA-seq analysis can be found here: > https://wiki.galaxyproject.org/Support#Tools_on_the_Main_server:_RNA-seq > > The QA/QC steps should be done before mapping, on individual > datasets (such as replicates) or on partial or merged datasets as > needed (if that is how the data was sequenced, just be > consistent). Only keep in mind that the larger the dataset, the > more compute some of these steps can require. > > Hopefully this helps, > > Jen > Galaxy team > > > On 1/1/14 1:32 AM, Elsayed Hejazy wrote: >> i need to know more about the order of steps for RNA Seq data >> analysis >> Is alignment and assembly should done first to combine all FASTQ >> reads into one file and start analysis or i should do Quality >> Control ,filtering , trimming and manipulation first and do >> alignment and assembly at the end of analysis to use tophat for >> example or any other analysis tools in Galaxy >> >> Thank you >> elsayed >> >> >> ___________________________________________________________ >> Please keep all replies on the list by using "reply all" >> in your mail client. To manage your subscriptions to this >> and other Galaxy lists, please use the interface at: >> http://lists.bx.psu.edu/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ > > -- > Jennifer Hillman-Jackson > http://galaxyproject.org > > -- Jennifer Hillman-Jackson http://galaxyproject.org

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