Re: [galaxy-dev] Error executing tool: 'hg19'
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. ___ 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/
Re: [galaxy-dev] Error executing tool: 'hg19'
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. ___ 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/
[galaxy-dev] Error executing tool: 'hg19'
Hi, 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. They all send this error message: Error executing tool: 'hg19' This bug has been reported before, but I was wondering if somebody suggest a fix for this? Thanks! Joachim. ___ 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/
Re: [galaxy-dev] Error executing tool: 'hg19'
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? 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 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? Thanks, J. ___ 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/
Re: [galaxy-dev] Error executing tool: 'hg19'
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. ___ 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/
