For completeness: this is a local galaxy instance running for few months now, updated recently (27 Jan 'release').

Hello Joachim,

...

After a quick try with visualising track in Trackster (importing one chromosome of hg19 - which did not succeed BTW), none of the tools in my local galaxy appear to work.

What are the steps you're taking to produce this issue?

I had a BAM file that I wanted to test to view with Trackster. I clicked that icon in the dataset . In the next screen: save in new visualation, which I called test. And I selected there 'Add a custom build'. Next I could select which fasta from my history containing the reference: selected the correct one. I named it "hg19_chrom21". But then, clicking OK, gave an error.

From then on, all tools give the error: Error executing tool: 'hg19'. The point is, I cannot recreate that BAM file, since the required tools are not working anymore... Basically, my Galaxy has become useless. Before I dig up my backup, I hope somebody can help me?

...

They all send this error message:

Error executing tool: 'hg19'

Are you seeing this error in failed datasets? If not, where are you seeing this error?

This error appears in the middle pane, after clicking execute.

...

This bug has been reported before, but I was wondering if somebody suggest a fix for this?

Can you provide a link to the thread/issue where this has been reported?

http://www.mail-archive.com/galaxy-dev@lists.bx.psu.edu/msg04216.html http://www.mail-archive.com/galaxy-dev@lists.bx.psu.edu/msg03995.html

Thanks, J.

Thank for looking into this.

First, thanks. I just created a new user, and I am ready to go with that user. FYI, the reset of the datatypes_conf.xml did not do the trick: following error appears on the custom builds page: NoConverterException: "Conversion from 'fasta' to 'len' not possible"

Thanks, Joachim

On 02/13/2012 06:02 PM, Jeremy Goecks wrote:

This bug has been fixed in galaxy-central but, as per one of the threads you found, has not made it to galaxy-dist yet.

Try this:

1. assuming you haven't made any changes to datatypes_conf.xml, copy datatypes_conf.xml.sample to datatypes_conf.xml
2. visit the custom builds page (User tab --> Custom Builds) and see if the Page loads properly; if it does, your custom build should work and everything should be fine.
3. this is a user-specific problem, so you can always create a new user and you should be good to go. If you want to continue to use the problematic account and the above doesn't work, you'll need to manually--via SQL--delete the user preferences for the problematic user.

Best, J.

On Feb 13, 2012, at 10:30 AM, Joachim Jacob wrote:

...

For completeness: this is a local galaxy instance running for few months now, updated recently (27 Jan 'release').

...

Hello Joachim,

...

After a quick try with visualising track in Trackster (importing one chromosome of hg19 - which did not succeed BTW), none of the tools in my local galaxy appear to work.

What are the steps you're taking to produce this issue?

I had a BAM file that I wanted to test to view with Trackster. I clicked that icon in the dataset . In the next screen: save in new visualation, which I called test. And I selected there 'Add a custom build'. Next I could select which fasta from my history containing the reference: selected the correct one. I named it "hg19_chrom21". But then, clicking OK, gave an error.

From then on, all tools give the error: Error executing tool: 'hg19'. The point is, I cannot recreate that BAM file, since the required tools are not working anymore... Basically, my Galaxy has become useless. Before I dig up my backup, I hope somebody can help me?

...

...

They all send this error message:

Error executing tool: 'hg19'

Are you seeing this error in failed datasets? If not, where are you seeing this error?

This error appears in the middle pane, after clicking execute.

...

...

This bug has been reported before, but I was wondering if somebody suggest a fix for this?

Can you provide a link to the thread/issue where this has been reported?

http://www.mail-archive.com/galaxy-dev@lists.bx.psu.edu/msg04216.html http://www.mail-archive.com/galaxy-dev@lists.bx.psu.edu/msg03995.html

...

Thanks, J.

Thank for looking into this.

These lines were not present in the datatypes_conf.xml <converter file="fasta_to_2bit.xml" target_datatype="twobit"/> <converter file="fasta_to_len.xml" target_datatype="len"/>

Actually, my datatypes_conf.xml was modified! I had added some lines to integrate RTG's mapper... (sorry for not mentioning this). I have added these lines to the new xml based on the .sample file, and restarted Galaxy. As my 'corrupted' user, I still get errors. BUT as my new user, I get the correct 'custom builds' page.

So actually, this work-around for the error is fine with me.

Joachim

Joachim Jacob, PhD Bioinformatics Training and Service facility VIB headquarters, Rijvisschestraat 120, BE-9052 Gent, Belgium (see map http://maps.google.be/maps/ms?ie=UTF8&hl=nl&msa=0&msid=110984434447938768012.00047d0caa7a96a740597&ll=51.017345,3.707585&spn=0.022003,0.043731&t=h&z=15)

Tel.: +32 9 244 66 34 | Fax.: +32 9 244 66 10

http://www.bits.vib.be/ http://www.vib.be/ http://be.linkedin.com/in/joachimjacob Skype Meâ?¢! skype:joachim.at.bits?call Follow bitsatvib on Twitter http://www.twitter.com/bitsatvib

On 02/14/2012 02:57 PM, Jeremy Goecks wrote:

Can you confirm that the following lines are in your datatypes_conf.xml file?

-- <datatype extension="fasta" type="galaxy.datatypes.sequence:Fasta" display_in_upload="true"> <converter file="fasta_to_tabular_converter.xml" target_datatype="tabular"/> <converter file="fasta_to_bowtie_base_index_converter.xml" target_datatype="bowtie_base_index"/> <converter file="fasta_to_bowtie_color_index_converter.xml" target_datatype="bowtie_color_index"/>

<converter file="fasta_to_2bit.xml" target_datatype="twobit"/> <converter file="fasta_to_len.xml" target_datatype="len"/> </datatype> --

If so, the other issue is that you'll need to restart Galaxy in order for the changes to take hold. Apologies for not mentioning this step previously.

J.

On Feb 14, 2012, at 3:18 AM, Joachim Jacob wrote:

...

First, thanks. I just created a new user, and I am ready to go with that user. FYI, the reset of the datatypes_conf.xml did not do the trick: following error appears on the custom builds page: NoConverterException: "Conversion from 'fasta' to 'len' not possible"

Thanks, Joachim

On 02/13/2012 06:02 PM, Jeremy Goecks wrote:

...

This bug has been fixed in galaxy-central but, as per one of the threads you found, has not made it to galaxy-dist yet.

Try this:

1. assuming you haven't made any changes to datatypes_conf.xml, copy datatypes_conf.xml.sample to datatypes_conf.xml
2. visit the custom builds page (User tab --> Custom Builds) and see if the Page loads properly; if it does, your custom build should work and everything should be fine.
3. this is a user-specific problem, so you can always create a new user and you should be good to go. If you want to continue to use the problematic account and the above doesn't work, you'll need to manually--via SQL--delete the user preferences for the problematic user.

Best, J.

On Feb 13, 2012, at 10:30 AM, Joachim Jacob wrote:

...

For completeness: this is a local galaxy instance running for few months now, updated recently (27 Jan 'release').

...

Hello Joachim,

...

After a quick try with visualising track in Trackster (importing one chromosome of hg19 - which did not succeed BTW), none of the tools in my local galaxy appear to work.

What are the steps you're taking to produce this issue?

I had a BAM file that I wanted to test to view with Trackster. I clicked that icon in the dataset . In the next screen: save in new visualation, which I called test. And I selected there 'Add a custom build'. Next I could select which fasta from my history containing the reference: selected the correct one. I named it "hg19_chrom21". But then, clicking OK, gave an error.

From then on, all tools give the error: Error executing tool: 'hg19'. The point is, I cannot recreate that BAM file, since the required tools are not working anymore... Basically, my Galaxy has become useless. Before I dig up my backup, I hope somebody can help me?

...

...

They all send this error message:

Error executing tool: 'hg19'

Are you seeing this error in failed datasets? If not, where are you seeing this error?

This error appears in the middle pane, after clicking execute.

...

...

This bug has been reported before, but I was wondering if somebody suggest a fix for this?

Can you provide a link to the thread/issue where this has been reported?

http://www.mail-archive.com/galaxy-dev@lists.bx.psu.edu/msg04216.html http://www.mail-archive.com/galaxy-dev@lists.bx.psu.edu/msg03995.html

...

Thanks, J.

Thank for looking into this.

Hi Paul,

Thanks for this suggestion, it would definitely make sense to create a reference to the actual workflow inputs in the new history. I'll see what I can do!

-Dannon

On Feb 14, 2012, at 11:05 AM, Paul Gordon wrote:

Hi all,

I have noticed that when I run a workflow with output to a new history, the data sets used as input to the workflow do not become part of the new history. Unfortunately, if a job fails in the workflow, the "rerun" interface for the job can't access the original data…it needs to be manually imported. While this is a minor annoyance, it becomes quite the pain if you ran the workflow for a bunch of input files. Can I put in a request that input data be imported automatically into workflow run histories, or have I missed something in the workflow run options?

Cheers,

Paul

---

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