HI
We have been struggling with this problem since we updated to "changeset:6799:40f1816d6857" (March 12, 2012 release). We never had the time to figure out whether it was a bug or whether we made a mistake. Unfortunately, it now has reached a point where we have a serious problem with our production server.
I managed to reproduce the error on a new galaxy-dist clone "changeset:7404:ec29ce8e27a1" (July 20, 2012 release):
I modify the top of "tool_conf.xml" in the following way (ie: adding a label):
<?xml version="1.0"?> <toolbox> <section name="Get Data" id="getext"> <tool file="data_source/upload.xml"/> <label text="external" id="external_data" /> <tool file="data_source/ucsc_tablebrowser.xml" /> <tool file="data_source/ucsc_tablebrowser_test.xml" /> ...
and it works, after restart, I get the label (see attachment "ss2.tiff")
I add a new tool definition: "load_abi_reads.xml":
<?xml version="1.0"?> <toolbox> <section name="Get Data" id="getext"> <tool file="data_source/upload.xml"/> <tool file="hrh/load_abi_reads.xml"/> <label text="external" id="external_data" /> <tool file="data_source/ucsc_tablebrowser.xml" /> <tool file="data_source/ucsc_tablebrowser_test.xml" /> ...
and it works, after restart, I get the new tool (see attachment "ss3.tiff")
Now, I don't like the label anymore
<toolbox> <section name="Get Data" id="getext"> <tool file="data_source/upload.xml"/> <tool file="hrh/load_abi_reads.xml"/> <!-- <label text="external" id="external_data" /> --> <tool file="data_source/ucsc_tablebrowser.xml" /> <tool file="data_source/ucsc_tablebrowser_test.xml" />
but, after restart, the label is still there.
Even worse, I add a second tool ("load_novaseq_reads.xml") before the first added tool
<?xml version="1.0"?> <toolbox> <section name="Get Data" id="getext"> <tool file="data_source/upload.xml"/> <tool file="hrh/load_novaseq_reads.xml"/> <tool file="hrh/load_abi_reads.xml"/> <!-- <label text="external" id="external_data" /> --> <tool file="data_source/ucsc_tablebrowser.xml" /> <tool file="data_source/ucsc_tablebrowser_test.xml" />
and after restart, the second tool is put below the first added tool (and the label is also still there, see attachment "ss4.tiff")
The display in the web browser corresponds to the file "integrated_tool_panel.xml", eg:
<?xml version="1.0"?> <toolbox> <section id="getext" name="Get Data" version=""> <tool id="upload1" /> <tool id="load_abi_reads" /> <tool id="load_novaseq_reads" /> <label id="external_data" text="external" version="" /> <tool id="ucsc_table_direct1" /> <tool id="ucsc_table_direct_test1" /> <tool id="ucsc_table_direct_archaea1" />
What do I need to change, in order to have the same information in the "integrated_tool_panel.xml" file as in the "tool_conf.xml" file with regard to order of the tools and removal of labels?
Any help appreciated
Thank you very much Regards, Hans
On Tue, Aug 21, 2012 at 4:18 PM, Hans-Rudolf Hotz hrh@fmi.ch wrote:
HI
We have been struggling with this problem since we updated to "changeset:6799:40f1816d6857" (March 12, 2012 release). We never had the time to figure out whether it was a bug or whether we made a mistake. Unfortunately, it now has reached a point where we have a serious problem with our production server.
I saw something funny like your screenshot of the funny with labels on our machine when I last modified our tool XML file. It seemed to be caching something from the old XML...
Note so far we've not installed anything automatically from the toolshed (just manually). I've not dug into the issue - just mentioning this as a clue that this is probably not unique to your Galaxy installation.
Regards,
Peter
Hello Hans-Rudolph,
If I remember correctly, the release in March did not properly handle the scenario where new tool entries were made within an existing section of the tool panel or new tool panel sections were added to specific locations of the tool panel. In both these cases, the new entry (tool or tool section) were appended to the end of the section or panel rather than inserted into the desired location. This is probably the cause of the behavior you are seeing. This issue was corrected in the next Galaxy release after the March release.
Greg Von Kuster
On Aug 21, 2012, at 2:03 PM, Peter Cock wrote:
On Tue, Aug 21, 2012 at 4:18 PM, Hans-Rudolf Hotz hrh@fmi.ch wrote:
HI
We have been struggling with this problem since we updated to "changeset:6799:40f1816d6857" (March 12, 2012 release). We never had the time to figure out whether it was a bug or whether we made a mistake. Unfortunately, it now has reached a point where we have a serious problem with our production server.
I saw something funny like your screenshot of the funny with labels on our machine when I last modified our tool XML file. It seemed to be caching something from the old XML...
Note so far we've not installed anything automatically from the toolshed (just manually). I've not dug into the issue - just mentioning this as a clue that this is probably not unique to your Galaxy installation.
Regards,
Peter ___________________________________________________________ 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 Greg
Thank you very much for your e-mail
Unfortunately, we still see this behavior in "changeset:7404:ec29ce8e27a1" (July 20, 2012 release).
All screen shots in my original e-mail (21-Aug) were made with a server running the July release.
Regards, Hans-Rudolf
On 08/27/2012 02:18 PM, Greg Von Kuster wrote:
Hello Hans-Rudolph,
If I remember correctly, the release in March did not properly handle the scenario where new tool entries were made within an existing section of the tool panel or new tool panel sections were added to specific locations of the tool panel. In both these cases, the new entry (tool or tool section) were appended to the end of the section or panel rather than inserted into the desired location. This is probably the cause of the behavior you are seeing. This issue was corrected in the next Galaxy release after the March release.
Greg Von Kuster
On Aug 21, 2012, at 2:03 PM, Peter Cock wrote:
On Tue, Aug 21, 2012 at 4:18 PM, Hans-Rudolf Hotz hrh@fmi.ch wrote:
HI
We have been struggling with this problem since we updated to "changeset:6799:40f1816d6857" (March 12, 2012 release). We never had the time to figure out whether it was a bug or whether we made a mistake. Unfortunately, it now has reached a point where we have a serious problem with our production server.
I saw something funny like your screenshot of the funny with labels on our machine when I last modified our tool XML file. It seemed to be caching something from the old XML...
Note so far we've not installed anything automatically from the toolshed (just manually). I've not dug into the issue - just mentioning this as a clue that this is probably not unique to your Galaxy installation.
Regards,
Peter ___________________________________________________________ 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:
I responded to your original email, which I should have done initially. Sorry for the back-and-forth on this.
On Aug 27, 2012, at 10:16 AM, Hans-Rudolf Hotz wrote:
Hi Greg
Thank you very much for your e-mail
Unfortunately, we still see this behavior in "changeset:7404:ec29ce8e27a1" (July 20, 2012 release).
All screen shots in my original e-mail (21-Aug) were made with a server running the July release.
Regards, Hans-Rudolf
On 08/27/2012 02:18 PM, Greg Von Kuster wrote:
Hello Hans-Rudolph,
If I remember correctly, the release in March did not properly handle the scenario where new tool entries were made within an existing section of the tool panel or new tool panel sections were added to specific locations of the tool panel. In both these cases, the new entry (tool or tool section) were appended to the end of the section or panel rather than inserted into the desired location. This is probably the cause of the behavior you are seeing. This issue was corrected in the next Galaxy release after the March release.
Greg Von Kuster
On Aug 21, 2012, at 2:03 PM, Peter Cock wrote:
On Tue, Aug 21, 2012 at 4:18 PM, Hans-Rudolf Hotz hrh@fmi.ch wrote:
HI
We have been struggling with this problem since we updated to "changeset:6799:40f1816d6857" (March 12, 2012 release). We never had the time to figure out whether it was a bug or whether we made a mistake. Unfortunately, it now has reached a point where we have a serious problem with our production server.
I saw something funny like your screenshot of the funny with labels on our machine when I last modified our tool XML file. It seemed to be caching something from the old XML...
Note so far we've not installed anything automatically from the toolshed (just manually). I've not dug into the issue - just mentioning this as a clue that this is probably not unique to your Galaxy installation.
Regards,
Peter ___________________________________________________________ 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 Hans,
Sorry, I missed your information about your using the latest dist release in my original response. See my inline comments.
On Aug 21, 2012, at 11:18 AM, Hans-Rudolf Hotz wrote:
HI
We have been struggling with this problem since we updated to "changeset:6799:40f1816d6857" (March 12, 2012 release). We never had the time to figure out whether it was a bug or whether we made a mistake. Unfortunately, it now has reached a point where we have a serious problem with our production server.
I managed to reproduce the error on a new galaxy-dist clone "changeset:7404:ec29ce8e27a1" (July 20, 2012 release):
I modify the top of "tool_conf.xml" in the following way (ie: adding a label):
<?xml version="1.0"?>
<toolbox> <section name="Get Data" id="getext"> <tool file="data_source/upload.xml"/> <label text="external" id="external_data" /> <tool file="data_source/ucsc_tablebrowser.xml" /> <tool file="data_source/ucsc_tablebrowser_test.xml" /> ...
and it works, after restart, I get the label (see attachment "ss2.tiff")
The above change will automatically be made to your integrated_tool_panel.xml, and this is why the behavior is as expected.
I add a new tool definition: "load_abi_reads.xml":
<?xml version="1.0"?>
<toolbox> <section name="Get Data" id="getext"> <tool file="data_source/upload.xml"/> <tool file="hrh/load_abi_reads.xml"/> <label text="external" id="external_data" /> <tool file="data_source/ucsc_tablebrowser.xml" /> <tool file="data_source/ucsc_tablebrowser_test.xml" /> ...
and it works, after restart, I get the new tool (see attachment "ss3.tiff")
The same comment I made above applies here as well.
Now, I don't like the label anymore
<toolbox> <section name="Get Data" id="getext"> <tool file="data_source/upload.xml"/> <tool file="hrh/load_abi_reads.xml"/> <!-- <label text="external" id="external_data" /> --> <tool file="data_source/ucsc_tablebrowser.xml" /> <tool file="data_source/ucsc_tablebrowser_test.xml" />
but, after restart, the label is still there.
If you commented this out in tool_conf.xml, it should have been eliminated automatically from integrated_tool_panel.xml when you restarted your Galaxy server. The fact that it wasn't may be a bug. I'll take a look at provide a fix asap if necessary.
Even worse, I add a second tool ("load_novaseq_reads.xml") before the first added tool
<?xml version="1.0"?>
<toolbox> <section name="Get Data" id="getext"> <tool file="data_source/upload.xml"/> <tool file="hrh/load_novaseq_reads.xml"/> <tool file="hrh/load_abi_reads.xml"/> <!-- <label text="external" id="external_data" /> --> <tool file="data_source/ucsc_tablebrowser.xml" /> <tool file="data_source/ucsc_tablebrowser_test.xml" />
and after restart, the second tool is put below the first added tool (and the label is also still there, see attachment "ss4.tiff")
I'll look at this as well and provide a fix asap if necessary.
The display in the web browser corresponds to the file "integrated_tool_panel.xml", eg:
<?xml version="1.0"?>
<toolbox> <section id="getext" name="Get Data" version=""> <tool id="upload1" /> <tool id="load_abi_reads" /> <tool id="load_novaseq_reads" /> <label id="external_data" text="external" version="" /> <tool id="ucsc_table_direct1" /> <tool id="ucsc_table_direct_test1" /> <tool id="ucsc_table_direct_archaea1" />
What do I need to change, in order to have the same information in the "integrated_tool_panel.xml" file as in the "tool_conf.xml" file with regard to order of the tools and removal of labels?
If you've not made any manual changes to your integrated_tool_panel.xml file, just delete it and it will be re-created automatically when you restart your Galaxy server. The layour of your tool panel will be as defined in your tool_conf.xml file. This is just a work-around assuming the above two issues are bugs that need to be fixed.
Any help appreciated
Thank you very much Regards, Hans
--
Hans-Rudolf Hotz, PhD Bioinformatics Support
Friedrich Miescher Institute for Biomedical Research Maulbeerstrasse 66 4058 Basel/Switzerland
<ss2.tiff><ss3.tiff><ss4.tiff>___________________________________________________________ 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 Greg
Thank you for your help. Although, "integrated_tool_panel.xml" is re-rewritten after each re-start, I can fix my problem (as you have suggested) by removing it first, and then do a restart.
Regards, Hans
On 08/27/2012 04:54 PM, Greg Von Kuster wrote:
Hi Hans,
Sorry, I missed your information about your using the latest dist release in my original response. See my inline comments.
On Aug 21, 2012, at 11:18 AM, Hans-Rudolf Hotz wrote:
HI
We have been struggling with this problem since we updated to "changeset:6799:40f1816d6857" (March 12, 2012 release). We never had the time to figure out whether it was a bug or whether we made a mistake. Unfortunately, it now has reached a point where we have a serious problem with our production server.
I managed to reproduce the error on a new galaxy-dist clone "changeset:7404:ec29ce8e27a1" (July 20, 2012 release):
I modify the top of "tool_conf.xml" in the following way (ie: adding a label):
<?xml version="1.0"?>
<toolbox> <section name="Get Data" id="getext"> <tool file="data_source/upload.xml"/> <label text="external" id="external_data" /> <tool file="data_source/ucsc_tablebrowser.xml" /> <tool file="data_source/ucsc_tablebrowser_test.xml" /> ...
and it works, after restart, I get the label (see attachment "ss2.tiff")
The above change will automatically be made to your integrated_tool_panel.xml, and this is why the behavior is as expected.
I add a new tool definition: "load_abi_reads.xml":
<?xml version="1.0"?>
<toolbox> <section name="Get Data" id="getext"> <tool file="data_source/upload.xml"/> <tool file="hrh/load_abi_reads.xml"/> <label text="external" id="external_data" /> <tool file="data_source/ucsc_tablebrowser.xml" /> <tool file="data_source/ucsc_tablebrowser_test.xml" /> ...
and it works, after restart, I get the new tool (see attachment "ss3.tiff")
The same comment I made above applies here as well.
Now, I don't like the label anymore
<toolbox> <section name="Get Data" id="getext"> <tool file="data_source/upload.xml"/> <tool file="hrh/load_abi_reads.xml"/> <!-- <label text="external" id="external_data" /> --> <tool file="data_source/ucsc_tablebrowser.xml" /> <tool file="data_source/ucsc_tablebrowser_test.xml" />
but, after restart, the label is still there.
If you commented this out in tool_conf.xml, it should have been eliminated automatically from integrated_tool_panel.xml when you restarted your Galaxy server. The fact that it wasn't may be a bug. I'll take a look at provide a fix asap if necessary.
Even worse, I add a second tool ("load_novaseq_reads.xml") before the first added tool
<?xml version="1.0"?>
<toolbox> <section name="Get Data" id="getext"> <tool file="data_source/upload.xml"/> <tool file="hrh/load_novaseq_reads.xml"/> <tool file="hrh/load_abi_reads.xml"/> <!-- <label text="external" id="external_data" /> --> <tool file="data_source/ucsc_tablebrowser.xml" /> <tool file="data_source/ucsc_tablebrowser_test.xml" />
and after restart, the second tool is put below the first added tool (and the label is also still there, see attachment "ss4.tiff")
I'll look at this as well and provide a fix asap if necessary.
The display in the web browser corresponds to the file "integrated_tool_panel.xml", eg:
<?xml version="1.0"?>
<toolbox> <section id="getext" name="Get Data" version=""> <tool id="upload1" /> <tool id="load_abi_reads" /> <tool id="load_novaseq_reads" /> <label id="external_data" text="external" version="" /> <tool id="ucsc_table_direct1" /> <tool id="ucsc_table_direct_test1" /> <tool id="ucsc_table_direct_archaea1" />
What do I need to change, in order to have the same information in the "integrated_tool_panel.xml" file as in the "tool_conf.xml" file with regard to order of the tools and removal of labels?
If you've not made any manual changes to your integrated_tool_panel.xml file, just delete it and it will be re-created automatically when you restart your Galaxy server. The layour of your tool panel will be as defined in your tool_conf.xml file. This is just a work-around assuming the above two issues are bugs that need to be fixed.
Any help appreciated
Thank you very much Regards, Hans
--
Hans-Rudolf Hotz, PhD Bioinformatics Support
Friedrich Miescher Institute for Biomedical Research Maulbeerstrasse 66 4058 Basel/Switzerland
<ss2.tiff><ss3.tiff><ss4.tiff>___________________________________________________________ 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 Hans,
I've committed a fix for this issue in changeset 7560:738b703f725c, which will be included in the next Galaxy release. Thanks for reporting this!
Greg Von Kuster
On Aug 28, 2012, at 5:40 AM, Hans-Rudolf Hotz wrote:
Hi Greg
Thank you for your help. Although, "integrated_tool_panel.xml" is re-rewritten after each re-start, I can fix my problem (as you have suggested) by removing it first, and then do a restart.
Regards, Hans
On 08/27/2012 04:54 PM, Greg Von Kuster wrote:
Hi Hans,
Sorry, I missed your information about your using the latest dist release in my original response. See my inline comments.
On Aug 21, 2012, at 11:18 AM, Hans-Rudolf Hotz wrote:
HI
We have been struggling with this problem since we updated to "changeset:6799:40f1816d6857" (March 12, 2012 release). We never had the time to figure out whether it was a bug or whether we made a mistake. Unfortunately, it now has reached a point where we have a serious problem with our production server.
I managed to reproduce the error on a new galaxy-dist clone "changeset:7404:ec29ce8e27a1" (July 20, 2012 release):
I modify the top of "tool_conf.xml" in the following way (ie: adding a label):
<?xml version="1.0"?>
<toolbox> <section name="Get Data" id="getext"> <tool file="data_source/upload.xml"/> <label text="external" id="external_data" /> <tool file="data_source/ucsc_tablebrowser.xml" /> <tool file="data_source/ucsc_tablebrowser_test.xml" /> ...
and it works, after restart, I get the label (see attachment "ss2.tiff")
The above change will automatically be made to your integrated_tool_panel.xml, and this is why the behavior is as expected.
I add a new tool definition: "load_abi_reads.xml":
<?xml version="1.0"?>
<toolbox> <section name="Get Data" id="getext"> <tool file="data_source/upload.xml"/> <tool file="hrh/load_abi_reads.xml"/> <label text="external" id="external_data" /> <tool file="data_source/ucsc_tablebrowser.xml" /> <tool file="data_source/ucsc_tablebrowser_test.xml" /> ...
and it works, after restart, I get the new tool (see attachment "ss3.tiff")
The same comment I made above applies here as well.
Now, I don't like the label anymore
<toolbox> <section name="Get Data" id="getext"> <tool file="data_source/upload.xml"/> <tool file="hrh/load_abi_reads.xml"/> <!-- <label text="external" id="external_data" /> --> <tool file="data_source/ucsc_tablebrowser.xml" /> <tool file="data_source/ucsc_tablebrowser_test.xml" />
but, after restart, the label is still there.
If you commented this out in tool_conf.xml, it should have been eliminated automatically from integrated_tool_panel.xml when you restarted your Galaxy server. The fact that it wasn't may be a bug. I'll take a look at provide a fix asap if necessary.
Even worse, I add a second tool ("load_novaseq_reads.xml") before the first added tool
<?xml version="1.0"?>
<toolbox> <section name="Get Data" id="getext"> <tool file="data_source/upload.xml"/> <tool file="hrh/load_novaseq_reads.xml"/> <tool file="hrh/load_abi_reads.xml"/> <!-- <label text="external" id="external_data" /> --> <tool file="data_source/ucsc_tablebrowser.xml" /> <tool file="data_source/ucsc_tablebrowser_test.xml" />
and after restart, the second tool is put below the first added tool (and the label is also still there, see attachment "ss4.tiff")
I'll look at this as well and provide a fix asap if necessary.
The display in the web browser corresponds to the file "integrated_tool_panel.xml", eg:
<?xml version="1.0"?>
<toolbox> <section id="getext" name="Get Data" version=""> <tool id="upload1" /> <tool id="load_abi_reads" /> <tool id="load_novaseq_reads" /> <label id="external_data" text="external" version="" /> <tool id="ucsc_table_direct1" /> <tool id="ucsc_table_direct_test1" /> <tool id="ucsc_table_direct_archaea1" />
What do I need to change, in order to have the same information in the "integrated_tool_panel.xml" file as in the "tool_conf.xml" file with regard to order of the tools and removal of labels?
If you've not made any manual changes to your integrated_tool_panel.xml file, just delete it and it will be re-created automatically when you restart your Galaxy server. The layour of your tool panel will be as defined in your tool_conf.xml file. This is just a work-around assuming the above two issues are bugs that need to be fixed.
Any help appreciated
Thank you very much Regards, Hans
--
Hans-Rudolf Hotz, PhD Bioinformatics Support
Friedrich Miescher Institute for Biomedical Research Maulbeerstrasse 66 4058 Basel/Switzerland
<ss2.tiff><ss3.tiff><ss4.tiff>___________________________________________________________ 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:
galaxy-dev@lists.galaxyproject.org
-
Greg Von Kuster -
Hans-Rudolf Hotz -
Peter Cock