Re: [galaxy-dev] Workflow import error
Hi Robert, I've cc'd the galaxy-dev list on this reply since the workflow components are primarily supported by other Galaxy development team members and I'm not optimally suited to handle this issue. Please keep responses on the galaxy-dev mail list so others that are interested can follow the entire thread. You should receive a response on this soon. Thanks for sending your messages, Greg Von Kuster On Apr 16, 2012, at 5:53 PM, Robert Chase wrote:
Hi Greg,
When I upload my workload ga file to galaxy, I get a screen saying that some of the tools in the workflow are not available in this instance of galaxy, specifically fastqc. I downloaded fastqc into my tools directory and restarted galaxy, but when I tried to re-upload the workflow it complained again that fastqc wasn't available. Fastqc does in fact load in the tools sidebar, but when I try to run it I get the following:
An error occurred running this job: Fastq failed. Error executing FastQC. /bin/sh: fastqc: command not found
-Rob
On Mon, Apr 16, 2012 at 10:21 AM, Greg Von Kuster <greg@bx.psu.edu> wrote: Hi Rob,
When you import a workflow into a Galaxy instance, the instance must have all tools required by the workflow available in its tool panel. I've only seen this error when the workflow requires a tool that is not available, so can you let us know if this is the case?
Thanks,
Greg Von Kuster
On Apr 16, 2012, at 10:07 AM, Robert Chase wrote:
Hi Greg,
After I modified the modules.py file that bug went away, but now I'm getting a new error:
Module galaxy.web.base.controller:420 in get_stored_workflow_steps view << module = module_factory.from_workflow_step( trans, step ) #Check if tool was upgraded step.upgrade_messages = module.check_and_update_state() # Any connected input needs to have value DummyDataset (these # are not persisted so we need to do it every time)>> step.upgrade_messages = module.check_and_update_state() AttributeError: 'NoneType' object has no attribute 'check_and_update_state'
-Rob
On Mon, Apr 16, 2012 at 9:19 AM, Robert Chase <rerpc@channing.harvard.edu> wrote: Thanks Greg,
I'll try to merge the change into my version.
-Rob
On Mon, Apr 16, 2012 at 9:18 AM, Greg Von Kuster <greg@bx.psu.edu> wrote: Hello Robert,
Thanks for reporting this issue - it has been fixed in change set 7038:1fdcce63a06f, which is currently available only in our central repository. It will be available in the dist in the next update.
Greg Von Kuster
On Apr 13, 2012, at 5:22 PM, Robert Chase wrote:
Hello All,
I'm pretty sure I found a bug in the main galaxy distribution. The following code diff shows the introduction of the line
tool_version = self.__get_tool_version( trans, tool_id )
but if you look at the function definition containing that line, you see
def from_workflow_step( Class, trans, step ): which does not half a self in it. Then we get an error.
-Rob ___________________________________________________________ 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:
Robert, It sounds like you're experiencing two separate problems to me. Let's isolating the problem to just the FastQC tool install, first, and move on from there. There is a FastQC tool in your toolbar, and execution results in the error you describe in the previous email of 'Fastq failed. Error executing FastQC. /bin/sh: fastqc command not found'. Correct? If this is the case, can you verify that you do have fastqc installed and accessible on the path of the galaxy user? And, how did you add the tool to galaxy- via toolshed or did you use the FastQC wrapper included with the primary Galaxy distribution? -Dannon On Apr 16, 2012, at 6:23 PM, Greg Von Kuster wrote:
Hi Robert,
I've cc'd the galaxy-dev list on this reply since the workflow components are primarily supported by other Galaxy development team members and I'm not optimally suited to handle this issue. Please keep responses on the galaxy-dev mail list so others that are interested can follow the entire thread. You should receive a response on this soon.
Thanks for sending your messages,
Greg Von Kuster
On Apr 16, 2012, at 5:53 PM, Robert Chase wrote:
Hi Greg,
When I upload my workload ga file to galaxy, I get a screen saying that some of the tools in the workflow are not available in this instance of galaxy, specifically fastqc. I downloaded fastqc into my tools directory and restarted galaxy, but when I tried to re-upload the workflow it complained again that fastqc wasn't available. Fastqc does in fact load in the tools sidebar, but when I try to run it I get the following:
An error occurred running this job: Fastq failed. Error executing FastQC. /bin/sh: fastqc: command not found
-Rob
On Mon, Apr 16, 2012 at 10:21 AM, Greg Von Kuster <greg@bx.psu.edu> wrote: Hi Rob,
When you import a workflow into a Galaxy instance, the instance must have all tools required by the workflow available in its tool panel. I've only seen this error when the workflow requires a tool that is not available, so can you let us know if this is the case?
Thanks,
Greg Von Kuster
On Apr 16, 2012, at 10:07 AM, Robert Chase wrote:
Hi Greg,
After I modified the modules.py file that bug went away, but now I'm getting a new error:
Module galaxy.web.base.controller:420 in get_stored_workflow_steps view << module = module_factory.from_workflow_step( trans, step ) #Check if tool was upgraded step.upgrade_messages = module.check_and_update_state() # Any connected input needs to have value DummyDataset (these # are not persisted so we need to do it every time)>> step.upgrade_messages = module.check_and_update_state() AttributeError: 'NoneType' object has no attribute 'check_and_update_state'
-Rob
On Mon, Apr 16, 2012 at 9:19 AM, Robert Chase <rerpc@channing.harvard.edu> wrote: Thanks Greg,
I'll try to merge the change into my version.
-Rob
On Mon, Apr 16, 2012 at 9:18 AM, Greg Von Kuster <greg@bx.psu.edu> wrote: Hello Robert,
Thanks for reporting this issue - it has been fixed in change set 7038:1fdcce63a06f, which is currently available only in our central repository. It will be available in the dist in the next update.
Greg Von Kuster
On Apr 13, 2012, at 5:22 PM, Robert Chase wrote:
Hello All,
I'm pretty sure I found a bug in the main galaxy distribution. The following code diff shows the introduction of the line
tool_version = self.__get_tool_version( trans, tool_id )
but if you look at the function definition containing that line, you see
def from_workflow_step( Class, trans, step ): which does not half a self in it. Then we get an error.
-Rob ___________________________________________________________ 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:
___________________________________________________________ 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:
Hello Dannon, I have downloaded the fastqc compiled program from http://www.bioinformatics.babraham.ac.uk/projects/download.html#fastqc I have added the directory containing the program fastqc to the path. The source version gave an error. Now I can successfully run the fastqc tool from the tool menu. I got this tool (the xml and python file) from the repository http://toolshed.g2.bx.psu.edu/repos/jjohnson/fastqc I tried deleting the uploaded workflow and uploading it again. I still get a screen complaining that it requires tools that are not available. When I click on the button for the tools, it says that fastqc is not available. The operative part of the .ga file is here I think: "tool_id": "fastqc", "tool_state": "{\"__page__\": 0, \"contaminants\": \"null\", \"chrom Info\": \"\\\"/galaxy/home/g2main/galaxy_main/tool-data/shared/ucsc/chrom/hg19.l en\\\"\", \"out_prefix\": \"\\\"FastQC\\\"\", \"input_file\": \"null\"}", "tool_version": "0.4", When I look at the fastqc tool xml file I see that the version is 1.0.0 <tool id="FastQC" name="FastQC" version="1.0.0"> <description>quality control checks on raw sequence data</description> <command interpreter="python">fastqc.py Could it be a version problem? Does the capitalization of the tool id matter? -Rob On Mon, Apr 16, 2012 at 9:31 PM, Dannon Baker <dannonbaker@me.com> wrote:
Robert,
It sounds like you're experiencing two separate problems to me. Let's isolating the problem to just the FastQC tool install, first, and move on from there. There is a FastQC tool in your toolbar, and execution results in the error you describe in the previous email of 'Fastq failed. Error executing FastQC. /bin/sh: fastqc command not found'. Correct?
If this is the case, can you verify that you do have fastqc installed and accessible on the path of the galaxy user? And, how did you add the tool to galaxy- via toolshed or did you use the FastQC wrapper included with the primary Galaxy distribution?
-Dannon
On Apr 16, 2012, at 6:23 PM, Greg Von Kuster wrote:
Hi Robert,
I've cc'd the galaxy-dev list on this reply since the workflow components are primarily supported by other Galaxy development team members and I'm not optimally suited to handle this issue. Please keep responses on the galaxy-dev mail list so others that are interested can follow the entire thread. You should receive a response on this soon.
Thanks for sending your messages,
Greg Von Kuster
On Apr 16, 2012, at 5:53 PM, Robert Chase wrote:
Hi Greg,
When I upload my workload ga file to galaxy, I get a screen saying that some of the tools in the workflow are not available in this instance of galaxy, specifically fastqc. I downloaded fastqc into my tools directory and restarted galaxy, but when I tried to re-upload the workflow it complained again that fastqc wasn't available. Fastqc does in fact load in the tools sidebar, but when I try to run it I get the following:
An error occurred running this job: Fastq failed. Error executing FastQC. /bin/sh: fastqc: command not found
-Rob
On Mon, Apr 16, 2012 at 10:21 AM, Greg Von Kuster <greg@bx.psu.edu> wrote: Hi Rob,
When you import a workflow into a Galaxy instance, the instance must have all tools required by the workflow available in its tool panel. I've only seen this error when the workflow requires a tool that is not available, so can you let us know if this is the case?
Thanks,
Greg Von Kuster
On Apr 16, 2012, at 10:07 AM, Robert Chase wrote:
Hi Greg,
After I modified the modules.py file that bug went away, but now I'm getting a new error:
Module galaxy.web.base.controller:420 in get_stored_workflow_steps view << module = module_factory.from_workflow_step( trans, step ) #Check if tool was upgraded step.upgrade_messages = module.check_and_update_state() # Any connected input needs to have value DummyDataset (these # are not persisted so we need to do it every time)>> step.upgrade_messages = module.check_and_update_state() AttributeError: 'NoneType' object has no attribute 'check_and_update_state'
-Rob
On Mon, Apr 16, 2012 at 9:19 AM, Robert Chase < rerpc@channing.harvard.edu> wrote: Thanks Greg,
I'll try to merge the change into my version.
-Rob
On Mon, Apr 16, 2012 at 9:18 AM, Greg Von Kuster <greg@bx.psu.edu> wrote: Hello Robert,
Thanks for reporting this issue - it has been fixed in change set 7038:1fdcce63a06f, which is currently available only in our central repository. It will be available in the dist in the next update.
Greg Von Kuster
On Apr 13, 2012, at 5:22 PM, Robert Chase wrote:
Hello All,
I'm pretty sure I found a bug in the main galaxy distribution. The following code diff shows the introduction of the line
tool_version = self.__get_tool_version( trans, tool_id )
but if you look at the function definition containing that line, you see
def from_workflow_step( Class, trans, step ): which does not half a self in it. Then we get an error.
-Rob ___________________________________________________________ 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:
___________________________________________________________ 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:
Hi, Robert. This is a longstanding wart - FastQC has to be invoked by a perl script distributed by the Babraham people - called simply 'fastqc'. To get this to work, the Galaxy FastQC wrapper expects that the FastQC distribution archive has been unpacked to tool-data/shared/jars/FastQC under your local Galaxy root. That means the fastqc perl script will be found at tool-data/shared/jars/FastQC/fastqc You will also need to make sure that the fastqc perl script that comes in the FastQC distribution is executable - I think the archive is made using windows so it needs tweaking to work under linux. Sorry this is so specific but we haven't come up with a better way of dealing with FastQC's specific requirements. I hope this helps? On Tue, Apr 17, 2012 at 4:12 PM, Robert Chase <rerpc@channing.harvard.edu> wrote:
Hello Dannon,
I have downloaded the fastqc compiled program from
http://www.bioinformatics.babraham.ac.uk/projects/download.html#fastqc
I have added the directory containing the program fastqc to the path. The source version gave an error.
Now I can successfully run the fastqc tool from the tool menu. I got this tool (the xml and python file) from the repository
http://toolshed.g2.bx.psu.edu/repos/jjohnson/fastqc
I tried deleting the uploaded workflow and uploading it again. I still get a screen complaining that it requires tools that are not available. When I click on the button for the tools, it says that fastqc is not available.
The operative part of the .ga file is here I think:
"tool_id": "fastqc", "tool_state": "{\"__page__\": 0, \"contaminants\": \"null\", \"chrom Info\": \"\\\"/galaxy/home/g2main/galaxy_main/tool-data/shared/ucsc/chrom/hg19.l en\\\"\", \"out_prefix\": \"\\\"FastQC\\\"\", \"input_file\": \"null\"}", "tool_version": "0.4",
When I look at the fastqc tool xml file I see that the version is 1.0.0
<tool id="FastQC" name="FastQC" version="1.0.0"> <description>quality control checks on raw sequence data</description> <command interpreter="python">fastqc.py
Could it be a version problem? Does the capitalization of the tool id matter?
-Rob
On Mon, Apr 16, 2012 at 9:31 PM, Dannon Baker <dannonbaker@me.com> wrote:
Robert,
It sounds like you're experiencing two separate problems to me. Let's isolating the problem to just the FastQC tool install, first, and move on from there. There is a FastQC tool in your toolbar, and execution results in the error you describe in the previous email of 'Fastq failed. Error executing FastQC. /bin/sh: fastqc command not found'. Correct?
If this is the case, can you verify that you do have fastqc installed and accessible on the path of the galaxy user? And, how did you add the tool to galaxy- via toolshed or did you use the FastQC wrapper included with the primary Galaxy distribution?
-Dannon
On Apr 16, 2012, at 6:23 PM, Greg Von Kuster wrote:
Hi Robert,
I've cc'd the galaxy-dev list on this reply since the workflow components are primarily supported by other Galaxy development team members and I'm not optimally suited to handle this issue. Please keep responses on the galaxy-dev mail list so others that are interested can follow the entire thread. You should receive a response on this soon.
Thanks for sending your messages,
Greg Von Kuster
On Apr 16, 2012, at 5:53 PM, Robert Chase wrote:
Hi Greg,
When I upload my workload ga file to galaxy, I get a screen saying that some of the tools in the workflow are not available in this instance of galaxy, specifically fastqc. I downloaded fastqc into my tools directory and restarted galaxy, but when I tried to re-upload the workflow it complained again that fastqc wasn't available. Fastqc does in fact load in the tools sidebar, but when I try to run it I get the following:
An error occurred running this job: Fastq failed. Error executing FastQC. /bin/sh: fastqc: command not found
-Rob
On Mon, Apr 16, 2012 at 10:21 AM, Greg Von Kuster <greg@bx.psu.edu> wrote: Hi Rob,
When you import a workflow into a Galaxy instance, the instance must have all tools required by the workflow available in its tool panel. I've only seen this error when the workflow requires a tool that is not available, so can you let us know if this is the case?
Thanks,
Greg Von Kuster
On Apr 16, 2012, at 10:07 AM, Robert Chase wrote:
Hi Greg,
After I modified the modules.py file that bug went away, but now I'm getting a new error:
Module galaxy.web.base.controller:420 in get_stored_workflow_steps view << module = module_factory.from_workflow_step( trans, step ) #Check if tool was upgraded step.upgrade_messages = module.check_and_update_state() # Any connected input needs to have value DummyDataset (these # are not persisted so we need to do it every time)>> step.upgrade_messages = module.check_and_update_state() AttributeError: 'NoneType' object has no attribute 'check_and_update_state'
-Rob
On Mon, Apr 16, 2012 at 9:19 AM, Robert Chase <rerpc@channing.harvard.edu> wrote: Thanks Greg,
I'll try to merge the change into my version.
-Rob
On Mon, Apr 16, 2012 at 9:18 AM, Greg Von Kuster <greg@bx.psu.edu> wrote: Hello Robert,
Thanks for reporting this issue - it has been fixed in change set 7038:1fdcce63a06f, which is currently available only in our central repository. It will be available in the dist in the next update.
Greg Von Kuster
On Apr 13, 2012, at 5:22 PM, Robert Chase wrote:
Hello All,
I'm pretty sure I found a bug in the main galaxy distribution. The following code diff shows the introduction of the line
tool_version = self.__get_tool_version( trans, tool_id )
but if you look at the function definition containing that line, you see
def from_workflow_step( Class, trans, step ): which does not half a self in it. Then we get an error.
-Rob ___________________________________________________________ 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:
___________________________________________________________ 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:
___________________________________________________________ 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:
-- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444;
participants (4)
-
Dannon Baker -
Greg Von Kuster -
Robert Chase -
Ross