Scott Tighe | 24 Apr 21:39 2014
Picon

Is the Server Down?

Jennifer

I have been trying to megablast some sequences for a few days now but it 
seems that the server is down. Can you advise?

Scott

--

-- 
Scott Tighe
Senior Core Laboratory Research Staff
Advanced Genome Technologies Core
NextGen Sequencing/Flow Cytometry
University of Vermont and Vermont Cancer Center
149 Beaumont ave
Health Science Research Facility 303/305
Burlington Vermont 05405
802-656-2482 (AGTC)

Peter Cock | 24 Apr 15:40 2014

BioStar integration - merging accounts

Hi all,

I see that https://biostar.usegalaxy.org is live now, with lots of
content mined from the galaxy-user mailing list (which may or may not
result in this email starting a new question? We shall see...).

Is it possible for an admin to merge accounts? e.g. there are all me:

https://biostar.usegalaxy.org/u/333/ - old ISP based email address
https://biostar.usegalaxy.org/u/337/ - old ISP based email address
https://biostar.usegalaxy.org/u/394/ - my Google mail address

Thanks,

Peter
Jennifer Jackson | 23 Apr 20:53 2014
Picon

Announcing the Galaxy Biostar Forum

Dear Galaxy Community,


Galaxy has teamed up with Biostar to create a Galaxy User support forum at https://biostar.usegalaxy.org!


We want to create a space where researchers using Galaxy can come together and share both scientific advice and practical tool help.  Whether on usegalaxy.org, a Cloudman instance, or any other Galaxy, if you have something to say about Using Galaxy, this is the place to do it!


Current integration with usegalaxy.org


Read more about how to get started at https://wiki.galaxyproject.org/Support/Biostar


Roll-out phase


What’s next


We hope you will like the change and look forward to any feedback you may have.


Thank you for using Galaxy!


Galaxy Team


<div>

      <p dir="ltr"><span>Dear
          Galaxy Community,</span></p>
      <br><span></span>
      <p dir="ltr"><span>Galaxy
          has teamed up with Biostar to create a Galaxy User support
          forum at </span><a href="https://biostar.usegalaxy.org/"><span>https://biostar.usegalaxy.org</span></a><span>!</span><span></span></p>
      <br><span></span>
      <p dir="ltr"><span>We
          want to create a space where researchers using Galaxy can come
          together and share both scientific advice and practical tool
          help. &nbsp;Whether on <a href="http://usegalaxy.org">usegalaxy.org</a>,
          a </span><a href="https://usegalaxy.org/cloud"><span></span></a><span><a href="http://usegalaxy.org/cloud">Cloudman</a> instance,
          or any <a href="https://wiki.galaxyproject.org/PublicGalaxyServers">other</a>
          <a href="http://getgalaxy.org">Galaxy</a>, if you have
          something to say about </span><span>Using
          Galaxy</span><span>,
          this is the place to do it!</span></p>
      <br><span></span>
      <p dir="ltr"><span>Current
          integration with usegalaxy.org</span></p>
      <ul>
<li dir="ltr">
          <p dir="ltr"><span>We
              imported the whole history of <a class="moz-txt-link-abbreviated" href="mailto:galaxy-user@...">galaxy-user@...</a>
              mailing list into Biostar</span></p>
        </li>
        <li dir="ltr">
          <p dir="ltr"><span>If
              you access Galaxy Biostar from <a href="http://usegalaxy.org">usegalaxy.org</a> (Top
                menu: "Help -&gt;Galaxy Biostar")</span><span>
              you will be automatically logged in. A Galaxy Biostar
              account will be created for you if it did not previously
              exist. To obtain this account&rsquo;s password please use the
              password reset feature of Galaxy Biostar (</span><a href="https://biostar.usegalaxy.org/accounts/password/reset/"><span>https://biostar.usegalaxy.org/accounts/password/reset/</span></a><span>).</span><span></span></p>
        </li>
        <li dir="ltr">
          <p dir="ltr"><span>When
              you have a question, search Biostar directly from any
              Galaxy tool page.</span></p>
        </li>
      </ul>
<br><span></span>
      <p dir="ltr"><span>Read
          more about </span><span>how
          to get started</span><span>
          at </span><a href="https://wiki.galaxyproject.org/Support/Biostar"><span>https://wiki.galaxyproject.org/Support/Biostar</span></a><span></span></p>
      <br><span></span>
      <p dir="ltr"><span>Roll-out
          phase</span></p>
      <ul>
<li dir="ltr">
          <p dir="ltr"><span>Galaxy
              Biostar is available at </span><a href="http://biostar.usegalaxy.org"><span>http://biostar.usegalaxy.org</span></a><span>
              and will be our primary avenue for support</span><span></span></p>
        </li>
        <li dir="ltr">
          <p dir="ltr"><span>The
              <a class="moz-txt-link-abbreviated" href="mailto:galaxy-user@...">galaxy-user@...</a> mailing list will continue to be
              supported during the transition</span><span>
            </span><span>but
              starting now </span><span>please
              use the </span><a href="http://biostar.usegalaxy.org"><span>biostar.usegalaxy.org</span></a><span>
            </span><span>forum</span><span>
              to ask all questions about using Galaxy.</span></p>
        </li>
        <li dir="ltr">
          <p dir="ltr"><span>
              Please </span><span>do
              not double post</span><span>
              to both Galaxy Biostar and <a class="moz-txt-link-abbreviated" href="mailto:galaxy-user@...">galaxy-user@...</a></span></p>
        </li>
        <li dir="ltr">
          <p dir="ltr"><span>
              Send us feedback through the forum's post "Welcome to
                Biostar" to tell us what you think.<br></span></p>
        </li>
      </ul>
<br><span></span>
      <p dir="ltr"><span>What&rsquo;s
          next</span></p>
      <ul>
<li dir="ltr">
          <p dir="ltr"><span>Notice
              will be given when the <a class="moz-txt-link-abbreviated" href="mailto:galaxy-user@...">galaxy-user@...</a> mailing list
              is retired. </span></p>
        </li>
        <li dir="ltr">
          <p dir="ltr"><span>Archives
              of <a class="moz-txt-link-abbreviated" href="mailto:galaxy-user@...">galaxy-user@...</a> will remain accessible. </span></p>
        </li>
      </ul>
<br><span></span>
      <p dir="ltr"><span>We
          hope you will like the change and look forward to any feedback
          you may have.</span></p>
      <br><span></span>
      <p dir="ltr"><span>Thank
          you for using Galaxy!</span></p>
      <br><span></span>
      <p dir="ltr"><a href="https://wiki.galaxyproject.org/GalaxyTeam"><span>Galaxy Team</span></a></p>
    <br class="Apple-interchange-newline">

  </div>
Matthew | 22 Apr 19:53 2014
Picon

'filter pileup' not working on 'generate pileup' output

   I used Bowtie2 on a fastq file. Then, generate pileup on the output 
of Bowtie2. When I try to use 'Filter pileup', there is no file 
recognized as input even though I have the output from the 'Generate 
pileup'.

Matthew
Sarah Maman | 22 Apr 12:25 2014
Picon
Picon

"Intersect multiple sorted BED files" / tool-data/shared/ucsc/chrom/genome_test.len) could not be opened

Hello,

I try to use "Intersect multiple sorted BED files" tool without success.
A genome_test have been added in galaxy (
genome_test.len in galaxy-dist/tool-data/shared/ucsc/chrom/, .fa and .dict added in .loc fils in tool-data/) but "Intersect multiple sorted BED files" gives this error message :
An error occurred running this job: Epilog : job finished at lun. mars 24 15:55:04 CET 2014
Error: The requested genome file (/..../galaxy-dist/tool-data/shared/ucsc/chrom/genome_test.len) could not be opened. Exiting!

So, I have integrated the code modification submitted in Galaxy Central (https://bitbucket.org/galaxy/galaxy-central/commits/7105c53139d4b8649e6a3714bc117118989712a2):
- chrom_info = os.path.join( trans.app.config.tool_data_path, 'shared','ucsc','chrom', "%s.len" % input_dbkey )
+ chrom_info = os.path.join( trans.app.config.len_file_path, "%s.len" % input_dbkey )

But I always have the same error message.

Could you please help us ?
Thanks in advance,
Sarah

-- --*-- Sarah Maman INRA - GenPhySE - SIGENAE http://www.sigenae.org/ Chemin de Borde-Rouge - Auzeville - BP 52627 31326 Castanet-Tolosan cedex - FRANCE Tel: +33(0)5.61.28.57.08 Fax: +33(0)5.61.28.57.53 --*--
<div>
Hello,<br><br>
I try to use <span class="link-bedtools_multiintersectbed tool-link">"Intersect
multiple sorted BED files" tool without success.<br>
A genome_test have been added in galaxy (</span><span class="link-bedtools_multiintersectbed tool-link">genome_test.len in </span><span class="link-bedtools_multiintersectbed tool-link">galaxy-dist/tool-data/shared/ucsc/chrom/,
.fa and .dict added in .loc fils in tool-data/) but </span><span class="link-bedtools_multiintersectbed tool-link">"Intersect multiple
sorted BED files" gives this error message :</span><br>
An error occurred running this job: Epilog : job finished at lun.
mars 24 15:55:04 CET 2014<br>
Error: The requested genome file
(/..../galaxy-dist/tool-data/shared/ucsc/chrom/genome_test.len)
could not be opened. Exiting!<br><br>
So, I have integrated the code modification submitted in Galaxy
Central
(<a class="moz-txt-link-freetext" href="https://bitbucket.org/galaxy/galaxy-central/commits/7105c53139d4b8649e6a3714bc117118989712a2">https://bitbucket.org/galaxy/galaxy-central/commits/7105c53139d4b8649e6a3714bc117118989712a2</a>):<br>-                chrom_info = os.path.join( trans.app.config.tool_data_path, 'shared','ucsc','chrom', "%s.len" % input_dbkey )
<div class="udiff-line addition" data-tnum="217">
<div class="gutter"> </div>
+                chrom_info = os.path.join( trans.app.config.len_file_path, "%s.len" % input_dbkey )
</div>
<br>
But I always have the same error message.<br><br>
Could you please help us ?<br>
Thanks in advance,<br>
Sarah<br><br>
--

-- 
          --*--
Sarah Maman
INRA - GenPhySE - SIGENAE
<a class="moz-txt-link-freetext" href="http://www.sigenae.org/">http://www.sigenae.org/</a>
Chemin de Borde-Rouge - Auzeville - BP 52627
31326 Castanet-Tolosan cedex - FRANCE
Tel:   +33(0)5.61.28.57.08
Fax:   +33(0)5.61.28.57.53 
         --*--
</div>
Carrie Gaut | 21 Apr 03:11 2014
Picon

Galaxy 101 tutorial

I'm working my way through the Galaxy 101 tutorial. I've run into a discrepancy when trying to "Get Data"
from the USC Main table browser. When trying to follow directions and choose the group, "variations and
repeats," it doesn't exist. I can choose variations OR I can choose repeats. This makes several of the
results not come out exactly as it shows they should and it makes steps further on in the tutorial
confusing. 

For me to get the correct tutorial results, which should I choose? Variations or repeats?

It may be that the tutorial was updated at some point but the tutorial directions and pictures were not. I
hope I've posted this in the correct mailing list... 

Sincerely, 
Carrie
Sent from my iPhone
Peng Yu | 19 Apr 06:16 2014
Picon

How many registered users are there at galaxy?

Hi,

I'm wondering how many registered users there are at galaxy. Is there
a way to check? Thanks.

--

-- 
Regards,
Peng
Tamara Simakova | 15 Apr 08:53 2014

bedtools error

Hello!

I'm using BedTools on the main Galaxy server. I try to use multiinter function to compare two bed files, but there is an error in the resulted file. Some coordinates that are present in both files are marked as they present only in one file. The bed-files format is correct. What could be the problem?

Thanks,
Tamara Simakova
Attachment (IAD39777_one-based_half-opened.bed): application/octet-stream, 1835 bytes
Attachment (new_bad_regions.bed): application/octet-stream, 599 bytes
<div><div dir="ltr">
<span>Hello!</span><div>
<span><br></span><div><span>I'm using BedTools on the main Galaxy server. I try to use multiinter function to compare two bed files, but there is an error in the resulted file. Some coordinates that are present in both files are marked as they present only in one file. The bed-files format is correct. What could be the problem?</span></div>
<div><span><br></span></div>
<div><span>Thanks,</span></div>
<div><span>Tamara Simakova</span></div>
</div>
</div></div>
Jennifer Jackson | 12 Apr 02:45 2014
Picon

trouble visualizing data

Hi Lindsey,

I see a few potential problem areas here. Double check these things:

1. when uploading, if the files are over 2G, or close to that, use FTP instead of a browser upload. Here is how: https://wiki.galaxyproject.org/FTPUpload

2. do not use the option to convert spaces to tabs. I doubt this does anything to a compressed format like BAM, but you almost never want to use this. Really is only for hand entered or pasted in data.

3. Try to convert the file to SAM to see if that functions. This will do two things: confirm basic BAM format is intact and permit you to examine the sequence identifiers on the header. Or try a tool like Picard's 'BAM Index Statistics'.

4. There could be an identifier mismatch problem between your data and our internal reference genome. The only ways to check are to either run some type of job that will list out our genome's sequences in the UI (like a small mapping job that creates a Galaxy-native BAM/SAM file) or obtain our version of the genome by rysnc and compare your files against it locally (before uploading to Galaxy). Both have advantages. The rsync server instructions are here, and I happened to use the genome question from yesterday to fill in the example last night, so you have near-exact instructions!
https://wiki.galaxyproject.org/Admin/UseGalaxyRsync

5. If all else fails, consider loading the genome that you used to do the mapping up to Galaxy as a Custom reference genome:
https://wiki.galaxyproject.org/Support#Custom_reference_genome
https://wiki.galaxyproject.org/Support#Reference_genomes

There have been some UI delays, but these are transient. Resubmitting the action has been working, so try that if buttons do not respond the first time.

Let us know if you continue to have problems,

Jen
Galaxy team

On 4/11/14 9:20 AM, Lindsey Fallis wrote:
Hi Jennifer, I’m a post doc working with Brenda Oppert (she contacted you yesterday with some problems). I too have been having some problems getting visualizations to work. My goal is to show the Tribolium genome as a Circster plot with my RNA-seq data laid on top. My RNA-seq data is currently in .bam format. So far what I have a attempted to do is upload my .bam files into Galaxy using the Get Data, upload file from computer functions. Then I choose my file, check the ‘convert spaces to tabs’ box and set the genome to Tcas. It uploads correctly. Then I ask it to visualize as Circster and nothing happens… Then I tried viewing in trackster and nothing happens OR I get an error message saying one of my sequences isn’t in the genome file. Any suggestions to get the visualizations to work so that I have the Tcas chromosomes as the Circster backbone and my RNA-seq data showing around it? Thank you! Lindsey

-- Jennifer Hillman-Jackson http://galaxyproject.org
<div>

    Hi Lindsey,<br><br>
    I see a few potential problem areas here. Double check these things:<br><br>
    1. when uploading, if the files are over 2G, or close to that, use
    FTP instead of a browser upload. Here is how:
    <a class="moz-txt-link-freetext" href="https://wiki.galaxyproject.org/FTPUpload">https://wiki.galaxyproject.org/FTPUpload</a><br><br>
    2. do not use the option to convert spaces to tabs. I doubt this
    does anything to a compressed format like BAM, but you almost never
    want to use this. Really is only for hand entered or pasted in data.<br><br>
    3. Try to convert the file to SAM to see if that functions. This
    will do two things: confirm basic BAM format is intact and permit
    you to examine the sequence identifiers on the header. Or try a tool
    like Picard's 'BAM Index Statistics'.<br><br>
    4. There could be an identifier mismatch problem between your data
    and our internal reference genome. The only ways to check are to
    either run some type of job that will list out our genome's
    sequences in the UI (like a small mapping job that creates a
    Galaxy-native BAM/SAM file) or obtain our version of the genome by
    rysnc and compare your files against it locally (before uploading to
    Galaxy). Both have advantages. The rsync server instructions are
    here, and I happened to use the genome question from yesterday to
    fill in the example last night, so you have near-exact instructions!
    <br><a class="moz-txt-link-freetext" href="https://wiki.galaxyproject.org/Admin/UseGalaxyRsync">https://wiki.galaxyproject.org/Admin/UseGalaxyRsync</a><br><br>
    5. If all else fails, consider loading the genome that you used to
    do the mapping up to Galaxy as a Custom reference genome:<br><a class="moz-txt-link-freetext" href="https://wiki.galaxyproject.org/Support#Custom_reference_genome">https://wiki.galaxyproject.org/Support#Custom_reference_genome</a><br><a class="moz-txt-link-freetext" href="https://wiki.galaxyproject.org/Support#Reference_genomes">https://wiki.galaxyproject.org/Support#Reference_genomes</a><br><br>
    There have been some UI delays, but these are transient.
    Resubmitting the action has been working, so try that if buttons do
    not respond the first time.<br><br>
    Let us know if you continue to have problems,<br><br>
    Jen<br>
    Galaxy team<br><br><div class="moz-cite-prefix">On 4/11/14 9:20 AM, Lindsey Fallis
      wrote:<br>
</div>
    <blockquote cite="mid:F7F88CB5-60DF-4B68-B689-22B77136DA77@..." type="cite">
      Hi Jennifer,

I&rsquo;m a post doc working with Brenda Oppert (she contacted you yesterday with some problems).  I too have been having some problems getting visualizations to work.  My goal is to show the Tribolium genome as a Circster plot with my RNA-seq data laid on top.  My RNA-seq data is currently in .bam format.  So far what I have a attempted to do is upload my .bam files into Galaxy using the Get Data, upload file from computer functions.  Then I choose my file, check the &lsquo;convert spaces to tabs&rsquo; box and set the genome to Tcas.  It uploads correctly.  Then I ask it to visualize as Circster and nothing happens&hellip;  Then I tried viewing in trackster and nothing happens OR I get an error message saying one of my sequences isn&rsquo;t in the genome file.  Any suggestions to get the visualizations to work so that I have the Tcas chromosomes as the Circster backbone and my RNA-seq data showing around it?

Thank you!
Lindsey

    </blockquote>
    <br>-- 
Jennifer Hillman-Jackson
<a class="moz-txt-link-freetext" href="http://galaxyproject.org">http://galaxyproject.org</a>
  </div>
Jennifer Jackson | 12 Apr 02:47 2014
Picon

trouble visualizing data

Hi Lindsey,

I see a few potential problem areas here. Double check these things:

1. when uploading, if the files are over 2G, or close to that, use FTP instead of a browser upload. Here is how: https://wiki.galaxyproject.org/FTPUpload

2. do not use the option to convert spaces to tabs. I doubt this does anything to a compressed format like BAM, but you almost never want to use this. Really is only for hand entered or pasted in data.

3. Try to convert the file to SAM to see if that functions. This will do two things: confirm basic BAM format is intact and permit you to examine the sequence identifiers on the header. Or try a tool like Picard's 'BAM Index Statistics'.

4. There could be an identifier mismatch problem between your data and our internal reference genome. The only ways to check are to either run some type of job that will list out our genome's sequences in the UI (like a small mapping job that creates a Galaxy-native BAM/SAM file) or obtain our version of the genome by rysnc and compare your files against it locally (before uploading to Galaxy). Both have advantages. The rsync server instructions are here, and I happened to use the genome question from yesterday to fill in the example last night, so you have near-exact instructions!
https://wiki.galaxyproject.org/Admin/UseGalaxyRsync

5. If all else fails, consider loading the genome that you used to do the mapping up to Galaxy as a Custom reference genome:
https://wiki.galaxyproject.org/Support#Custom_reference_genome
https://wiki.galaxyproject.org/Support#Reference_genomes

There have been some UI delays, but these are transient. Resubmitting the action has been working, so try that if buttons do not respond the first time.

Let us know if you continue to have problems,

Jen
Galaxy team

On 4/11/14 9:20 AM, Lindsey Fallis wrote:
Hi Jennifer, I’m a post doc working with Brenda Oppert (she contacted you yesterday with some problems). I too have been having some problems getting visualizations to work. My goal is to show the Tribolium genome as a Circster plot with my RNA-seq data laid on top. My RNA-seq data is currently in .bam format. So far what I have a attempted to do is upload my .bam files into Galaxy using the Get Data, upload file from computer functions. Then I choose my file, check the ‘convert spaces to tabs’ box and set the genome to Tcas. It uploads correctly. Then I ask it to visualize as Circster and nothing happens… Then I tried viewing in trackster and nothing happens OR I get an error message saying one of my sequences isn’t in the genome file. Any suggestions to get the visualizations to work so that I have the Tcas chromosomes as the Circster backbone and my RNA-seq data showing around it? Thank you! Lindsey

-- Jennifer Hillman-Jackson http://galaxyproject.org
<div>

    Hi Lindsey,<br><br>
    I see a few potential problem areas here. Double check these things:<br><br>
    1. when uploading, if the files are over 2G, or close to that, use
    FTP instead of a browser upload. Here is how:
    <a class="moz-txt-link-freetext" href="https://wiki.galaxyproject.org/FTPUpload">https://wiki.galaxyproject.org/FTPUpload</a><br><br>
    2. do not use the option to convert spaces to tabs. I doubt this
    does anything to a compressed format like BAM, but you almost never
    want to use this. Really is only for hand entered or pasted in data.<br><br>
    3. Try to convert the file to SAM to see if that functions. This
    will do two things: confirm basic BAM format is intact and permit
    you to examine the sequence identifiers on the header. Or try a tool
    like Picard's 'BAM Index Statistics'.<br><br>
    4. There could be an identifier mismatch problem between your data
    and our internal reference genome. The only ways to check are to
    either run some type of job that will list out our genome's
    sequences in the UI (like a small mapping job that creates a
    Galaxy-native BAM/SAM file) or obtain our version of the genome by
    rysnc and compare your files against it locally (before uploading to
    Galaxy). Both have advantages. The rsync server instructions are
    here, and I happened to use the genome question from yesterday to
    fill in the example last night, so you have near-exact instructions!
    <br><a class="moz-txt-link-freetext" href="https://wiki.galaxyproject.org/Admin/UseGalaxyRsync">https://wiki.galaxyproject.org/Admin/UseGalaxyRsync</a><br><br>
    5. If all else fails, consider loading the genome that you used to
    do the mapping up to Galaxy as a Custom reference genome:<br><a class="moz-txt-link-freetext" href="https://wiki.galaxyproject.org/Support#Custom_reference_genome">https://wiki.galaxyproject.org/Support#Custom_reference_genome</a><br><a class="moz-txt-link-freetext" href="https://wiki.galaxyproject.org/Support#Reference_genomes">https://wiki.galaxyproject.org/Support#Reference_genomes</a><br><br>
    There have been some UI delays, but these are transient.
    Resubmitting the action has been working, so try that if buttons do
    not respond the first time.<br><br>
    Let us know if you continue to have problems,<br><br>
    Jen<br>
    Galaxy team<br><br><div class="moz-cite-prefix">On 4/11/14 9:20 AM, Lindsey Fallis
      wrote:<br>
</div>
    <blockquote cite="mid:F7F88CB5-60DF-4B68-B689-22B77136DA77@..." type="cite">
      Hi Jennifer,

I&rsquo;m a post doc working with Brenda Oppert (she contacted you yesterday with some problems).  I too have been having some problems getting visualizations to work.  My goal is to show the Tribolium genome as a Circster plot with my RNA-seq data laid on top.  My RNA-seq data is currently in .bam format.  So far what I have a attempted to do is upload my .bam files into Galaxy using the Get Data, upload file from computer functions.  Then I choose my file, check the &lsquo;convert spaces to tabs&rsquo; box and set the genome to Tcas.  It uploads correctly.  Then I ask it to visualize as Circster and nothing happens&hellip;  Then I tried viewing in trackster and nothing happens OR I get an error message saying one of my sequences isn&rsquo;t in the genome file.  Any suggestions to get the visualizations to work so that I have the Tcas chromosomes as the Circster backbone and my RNA-seq data showing around it?

Thank you!
Lindsey

    </blockquote>
    <br>-- 
Jennifer Hillman-Jackson
<a class="moz-txt-link-freetext" href="http://galaxyproject.org">http://galaxyproject.org</a>
  </div>
KS | 12 Apr 00:16 2014
Picon

Base Recalibration tool on usegalaxy

Dear all,

I can't find either of Table Recalibration or Base Recalibrator on
usegalaxy public server. I am defident this is right place to ask, but
seqanswers is clouded with many other pipelines.

Is there an update of base recalibration tool on usegalaxy?

Best,
Kaz

Gmane