Hi all,
The download URL seems not to be accepted in tool_dependencies.xml. It is an URL from sourceforge, the direct link to a package.
The error upon uploading the tool to my toolshed: ************** Metadata may have been defined for some items in revision '5665a799775d'. Correct the following problems if necessary and reset metadata. tool_dependencies.xml - Exception attempting to parse /mnt/toolsheddb/database/000/repo_26/tool_dependencies.xml: not well-formed (invalid token): line 6, column 149 **************
The tool_dependencies.xml file: ************** 1 <?xml version="1.0"?> 2 <tool_dependency> 3 <package name="transpose" version="2.0.0"> 4 <install version="1.0"> 5 <actions> 6 <action type="download_by_url">http://downloads.sourceforge.net/project/transpose/transpose/transpose-2.0/2...</action> 7 <action type="shell_command">mkdir bin</action> 8 <action type="shell_command">unzip transpose-2.0.zip</action> <action type="shell_command">cd transpose-2.0/src</action> <action type="shell_command">gcc transpose.c -o transpose</action> <action type="move_file"> <source>$INSTALL_DIR/transpose-2.0/src/transpose</source> <destination>$INSTALL_DIR/bin</destination> </action> <action type="shell_command">chmod +x $INSTALL_DIR/bin/transpose</action> <action type="set_environment"> <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> </action> </actions> </install> <readme> Compiling transpose and putting in the path. </readme> </package> </tool_dependency> **************
Cheers, Joachim
This problem is probably due to the 2 ampersands '&', which are not allowed in XML. Try substituting them with '&'.
Nicola
Il giorno lun, 30/09/2013 alle 13.51 +0200, Joachim Jacob | VIB | ha scritto:
Hi all,
The download URL seems not to be accepted in tool_dependencies.xml. It is an URL from sourceforge, the direct link to a package.
The error upon uploading the tool to my toolshed:
Metadata may have been defined for some items in revision '5665a799775d'. Correct the following problems if necessary and reset metadata. tool_dependencies.xml - Exception attempting to parse /mnt/toolsheddb/database/000/repo_26/tool_dependencies.xml: not well-formed (invalid token): line 6, column 149
The tool_dependencies.xml file:
1 <?xml version="1.0"?> 2 <tool_dependency> 3 <package name="transpose" version="2.0.0"> 4 <install version="1.0"> 5 <actions> 6 <action type="download_by_url">http://downloads.sourceforge.net/project/transpose/transpose/transpose-2.0/2...</action> 7 <action type="shell_command">mkdir bin</action> 8 <action type="shell_command">unzip transpose-2.0.zip</action> <action type="shell_command">cd transpose-2.0/src</action> <action type="shell_command">gcc transpose.c -o transpose</action> <action type="move_file">
<source>$INSTALL_DIR/transpose-2.0/src/transpose</source> <destination>$INSTALL_DIR/bin</destination> </action> <action type="shell_command">chmod +x $INSTALL_DIR/bin/transpose</action> <action type="set_environment"> <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> </action> </actions> </install> <readme> Compiling transpose and putting in the path. </readme> </package> </tool_dependency> **************
Cheers, Joachim
Hi Joachim,
try to remove the last part '?r=&ts=1380535239&use_mirror=surfnet'
Cheers, Bjoern
Hi all,
The download URL seems not to be accepted in tool_dependencies.xml. It is an URL from sourceforge, the direct link to a package.
The error upon uploading the tool to my toolshed:
Metadata may have been defined for some items in revision '5665a799775d'. Correct the following problems if necessary and reset metadata. tool_dependencies.xml - Exception attempting to parse /mnt/toolsheddb/database/000/repo_26/tool_dependencies.xml: not well-formed (invalid token): line 6, column 149
The tool_dependencies.xml file:
1 <?xml version="1.0"?> 2 <tool_dependency> 3 <package name="transpose" version="2.0.0"> 4 <install version="1.0"> 5 <actions> 6 <action type="download_by_url">http://downloads.sourceforge.net/project/transpose/transpose/transpose-2.0/2...</action> 7 <action type="shell_command">mkdir bin</action> 8 <action type="shell_command">unzip transpose-2.0.zip</action> <action type="shell_command">cd transpose-2.0/src</action> <action type="shell_command">gcc transpose.c -o transpose</action> <action type="move_file">
<source>$INSTALL_DIR/transpose-2.0/src/transpose</source> <destination>$INSTALL_DIR/bin</destination> </action> <action type="shell_command">chmod +x $INSTALL_DIR/bin/transpose</action> <action type="set_environment"> <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> </action> </actions> </install> <readme> Compiling transpose and putting in the path. </readme> </package> </tool_dependency> **************
Cheers, Joachim
You must escape any ampersand in the XML as & and then it should work.
Peter
On Mon, Sep 30, 2013 at 12:51 PM, Joachim Jacob | VIB | joachim.jacob@vib.be wrote:
Hi all,
The download URL seems not to be accepted in tool_dependencies.xml. It is an URL from sourceforge, the direct link to a package.
The error upon uploading the tool to my toolshed:
Metadata may have been defined for some items in revision '5665a799775d'. Correct the following problems if necessary and reset metadata. tool_dependencies.xml - Exception attempting to parse /mnt/toolsheddb/database/000/repo_26/tool_dependencies.xml: not well-formed (invalid token): line 6, column 149
The tool_dependencies.xml file:
1 <?xml version="1.0"?> 2 <tool_dependency> 3 <package name="transpose" version="2.0.0"> 4 <install version="1.0"> 5 <actions> 6 <action type="download_by_url">http://downloads.sourceforge.net/project/transpose/transpose/transpose-2.0/2...</action> 7 <action type="shell_command">mkdir bin</action> 8 <action type="shell_command">unzip transpose-2.0.zip</action> <action type="shell_command">cd transpose-2.0/src</action> <action type="shell_command">gcc transpose.c -o transpose</action> <action type="move_file">
<source>$INSTALL_DIR/transpose-2.0/src/transpose</source> <destination>$INSTALL_DIR/bin</destination> </action> <action type="shell_command">chmod +x $INSTALL_DIR/bin/transpose</action> <action type="set_environment"> <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> </action> </actions> </install> <readme> Compiling transpose and putting in the path. </readme> </package> </tool_dependency> **************
Cheers, Joachim
-- Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team
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/
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Hi all,
Not fixed yet. Somehow the download does not work: I have escaped the ampersands and the hyphens. The download seems to have to proceed, since I receive no error from the download step. The next step in the dependencies file gives an error: mv: cannot stat transpose.zip': No such file or directory
Cheers, J
Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team
On 09/30/2013 02:06 PM, Peter Cock wrote:
You must escape any ampersand in the XML as & and then it should work.
Peter
On Mon, Sep 30, 2013 at 12:51 PM, Joachim Jacob | VIB | joachim.jacob@vib.be wrote:
Hi all,
The download URL seems not to be accepted in tool_dependencies.xml. It is an URL from sourceforge, the direct link to a package.
The error upon uploading the tool to my toolshed:
Metadata may have been defined for some items in revision '5665a799775d'. Correct the following problems if necessary and reset metadata. tool_dependencies.xml - Exception attempting to parse /mnt/toolsheddb/database/000/repo_26/tool_dependencies.xml: not well-formed (invalid token): line 6, column 149
The tool_dependencies.xml file:
1 <?xml version="1.0"?> 2 <tool_dependency> 3 <package name="transpose" version="2.0.0"> 4 <install version="1.0"> 5 <actions> 6 <action type="download_by_url">http://downloads.sourceforge.net/project/transpose/transpose/transpose-2.0/2...</action> 7 <action type="shell_command">mkdir bin</action> 8 <action type="shell_command">unzip transpose-2.0.zip</action> <action type="shell_command">cd transpose-2.0/src</action> <action type="shell_command">gcc transpose.c -o transpose</action> <action type="move_file">
<source>$INSTALL_DIR/transpose-2.0/src/transpose</source> <destination>$INSTALL_DIR/bin</destination> </action> <action type="shell_command">chmod +x $INSTALL_DIR/bin/transpose</action> <action type="set_environment"> <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> </action> </actions> </install> <readme> Compiling transpose and putting in the path. </readme> </package> </tool_dependency> **************
Cheers, Joachim
-- Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team
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/
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Joachim,
For sourceforge URLs, you can safely omit the question mark and everything after it, since that's part of the browser download load balancing process. When downloading with wget, curl, or python's urllib, downloads.sourceforge.net does its own behind-the-scenes load balancing. As for hyphens, I don't believe they need to be escaped, since they're not XML entities like the ampersand is. The following download_by_url action should work:
<action type="download_by_url">http://downloads.sourceforge.net/project/transpose/transpose/transpose-2.0/2...</action>
--Dave B.
On 09/30/2013 08:45 AM, Joachim Jacob | VIB | wrote:
Hi all,
Not fixed yet. Somehow the download does not work: I have escaped the ampersands and the hyphens. The download seems to have to proceed, since I receive no error from the download step. The next step in the dependencies file gives an error: mv: cannot stat transpose.zip': No such file or directory
Cheers, J
Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team
On 09/30/2013 02:06 PM, Peter Cock wrote:
You must escape any ampersand in the XML as & and then it should work.
Peter
On Mon, Sep 30, 2013 at 12:51 PM, Joachim Jacob | VIB | joachim.jacob@vib.be wrote:
Hi all,
The download URL seems not to be accepted in tool_dependencies.xml. It is an URL from sourceforge, the direct link to a package.
The error upon uploading the tool to my toolshed:
Metadata may have been defined for some items in revision '5665a799775d'. Correct the following problems if necessary and reset metadata. tool_dependencies.xml - Exception attempting to parse /mnt/toolsheddb/database/000/repo_26/tool_dependencies.xml: not well-formed (invalid token): line 6, column 149
The tool_dependencies.xml file:
1 <?xml version="1.0"?> 2 <tool_dependency> 3 <package name="transpose" version="2.0.0"> 4 <install version="1.0"> 5 <actions> 6 <action type="download_by_url">http://downloads.sourceforge.net/project/transpose/transpose/transpose-2.0/2...</action>
7 <action type="shell_command">mkdir bin</action> 8 <action type="shell_command">unzip transpose-2.0.zip</action> <action type="shell_command">cd transpose-2.0/src</action> <action type="shell_command">gcc transpose.c -o transpose</action> <action type="move_file">
<source>$INSTALL_DIR/transpose-2.0/src/transpose</source> <destination>$INSTALL_DIR/bin</destination> </action> <action type="shell_command">chmod +x $INSTALL_DIR/bin/transpose</action> <action type="set_environment"> <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> </action> </actions> </install> <readme> Compiling transpose and putting in the path. </readme> </package> </tool_dependency> **************
Cheers, Joachim
-- Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team
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/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
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/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Still having a hard time and some strange situations. It is almost too much to report via email.
Basically, the tool_dependencies.xml get recognised sometimes. Please, watch this video to see what I mean (1'30''), and pause as you like: https://dl.dropboxusercontent.com/u/18352887/toolshedissues.ogv
I am afraid I cannot invest this amount of time to make my repo's public-proof. There are weird things happening which make no sense to me. And debugging of tool_dependencies.xml is very hard, since I find almost no logs of this process.
Joachim.
Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team
On 09/30/2013 02:53 PM, Dave Bouvier wrote:
Joachim,
For sourceforge URLs, you can safely omit the question mark and everything after it, since that's part of the browser download load balancing process. When downloading with wget, curl, or python's urllib, downloads.sourceforge.net does its own behind-the-scenes load balancing. As for hyphens, I don't believe they need to be escaped, since they're not XML entities like the ampersand is. The following download_by_url action should work:
<action type="download_by_url">http://downloads.sourceforge.net/project/transpose/transpose/transpose-2.0/2...</action>
--Dave B.
On 09/30/2013 08:45 AM, Joachim Jacob | VIB | wrote:
Hi all,
Not fixed yet. Somehow the download does not work: I have escaped the ampersands and the hyphens. The download seems to have to proceed, since I receive no error from the download step. The next step in the dependencies file gives an error: mv: cannot stat transpose.zip': No such file or directory
Cheers, J
Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team
On 09/30/2013 02:06 PM, Peter Cock wrote:
You must escape any ampersand in the XML as & and then it should work.
Peter
On Mon, Sep 30, 2013 at 12:51 PM, Joachim Jacob | VIB | joachim.jacob@vib.be wrote:
Hi all,
The download URL seems not to be accepted in tool_dependencies.xml. It is an URL from sourceforge, the direct link to a package.
The error upon uploading the tool to my toolshed:
Metadata may have been defined for some items in revision '5665a799775d'. Correct the following problems if necessary and reset metadata. tool_dependencies.xml - Exception attempting to parse /mnt/toolsheddb/database/000/repo_26/tool_dependencies.xml: not well-formed (invalid token): line 6, column 149
The tool_dependencies.xml file:
1 <?xml version="1.0"?> 2 <tool_dependency> 3 <package name="transpose" version="2.0.0"> 4 <install version="1.0"> 5 <actions> 6 <action type="download_by_url">http://downloads.sourceforge.net/project/transpose/transpose/transpose-2.0/2...</action>
7 <action type="shell_command">mkdir bin</action> 8 <action type="shell_command">unzip transpose-2.0.zip</action> <action type="shell_command">cd transpose-2.0/src</action> <action type="shell_command">gcc transpose.c -o transpose</action> <action type="move_file">
<source>$INSTALL_DIR/transpose-2.0/src/transpose</source> <destination>$INSTALL_DIR/bin</destination> </action> <action type="shell_command">chmod +x $INSTALL_DIR/bin/transpose</action> <action type="set_environment"> <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> </action> </actions> </install> <readme> Compiling transpose and putting in the path. </readme> </package> </tool_dependency> **************
Cheers, Joachim
-- Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team
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/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
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/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Hi Joachim,
I had such problems if my XML file is invalid. Than I get immediately the 'installed:' text and can click install again, without any change. Also I would really recommend to reset your toolshed. These "white ghosts" can have unpredictable effects.
If you can upload your tools to the test tool shed I can try to install it debug it.
Please make sure that you run the latest Galaxy central version. Greg and Dave invested a lot of time to get rid of "white ghosts". But these changes are only in central.
Cheers, Bjoern
Still having a hard time and some strange situations. It is almost too much to report via email.
Basically, the tool_dependencies.xml get recognised sometimes. Please, watch this video to see what I mean (1'30''), and pause as you like: https://dl.dropboxusercontent.com/u/18352887/toolshedissues.ogv
I am afraid I cannot invest this amount of time to make my repo's public-proof. There are weird things happening which make no sense to me. And debugging of tool_dependencies.xml is very hard, since I find almost no logs of this process.
Joachim.
Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team
On 09/30/2013 02:53 PM, Dave Bouvier wrote:
Joachim,
For sourceforge URLs, you can safely omit the question mark and everything after it, since that's part of the browser download load balancing process. When downloading with wget, curl, or python's urllib, downloads.sourceforge.net does its own behind-the-scenes load balancing. As for hyphens, I don't believe they need to be escaped, since they're not XML entities like the ampersand is. The following download_by_url action should work:
<action type="download_by_url">http://downloads.sourceforge.net/project/transpose/transpose/transpose-2.0/2...</action>
--Dave B.
On 09/30/2013 08:45 AM, Joachim Jacob | VIB | wrote:
Hi all,
Not fixed yet. Somehow the download does not work: I have escaped the ampersands and the hyphens. The download seems to have to proceed, since I receive no error from the download step. The next step in the dependencies file gives an error: mv: cannot stat transpose.zip': No such file or directory
Cheers, J
Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team
On 09/30/2013 02:06 PM, Peter Cock wrote:
You must escape any ampersand in the XML as & and then it should work.
Peter
On Mon, Sep 30, 2013 at 12:51 PM, Joachim Jacob | VIB | joachim.jacob@vib.be wrote:
Hi all,
The download URL seems not to be accepted in tool_dependencies.xml. It is an URL from sourceforge, the direct link to a package.
The error upon uploading the tool to my toolshed:
Metadata may have been defined for some items in revision '5665a799775d'. Correct the following problems if necessary and reset metadata. tool_dependencies.xml - Exception attempting to parse /mnt/toolsheddb/database/000/repo_26/tool_dependencies.xml: not well-formed (invalid token): line 6, column 149
The tool_dependencies.xml file:
1 <?xml version="1.0"?> 2 <tool_dependency> 3 <package name="transpose" version="2.0.0"> 4 <install version="1.0"> 5 <actions> 6 <action type="download_by_url">http://downloads.sourceforge.net/project/transpose/transpose/transpose-2.0/2...</action>
7 <action type="shell_command">mkdir bin</action> 8 <action type="shell_command">unzip transpose-2.0.zip</action> <action type="shell_command">cd transpose-2.0/src</action> <action type="shell_command">gcc transpose.c -o transpose</action> <action type="move_file">
<source>$INSTALL_DIR/transpose-2.0/src/transpose</source> <destination>$INSTALL_DIR/bin</destination> </action> <action type="shell_command">chmod +x $INSTALL_DIR/bin/transpose</action> <action type="set_environment"> <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> </action> </actions> </install> <readme> Compiling transpose and putting in the path. </readme> </package> </tool_dependency> **************
Cheers, Joachim
-- Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team
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/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
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/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Thanks, then I will run toolshed from a separate galaxy-central clone if that's advisable - different from the Galaxy service. I prefer to keep galaxy-dist on the stable branch.
In this process, I will move the tools from the old toolshed to my new toolshed running from galaxy-central. When I have time, I will upload everything to the test-toolshed.
Cheers, Joachim
Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team
On 09/30/2013 05:11 PM, Bjoern Gruening wrote:
Hi Joachim,
I had such problems if my XML file is invalid. Than I get immediately the 'installed:' text and can click install again, without any change. Also I would really recommend to reset your toolshed. These "white ghosts" can have unpredictable effects.
If you can upload your tools to the test tool shed I can try to install it debug it.
Please make sure that you run the latest Galaxy central version. Greg and Dave invested a lot of time to get rid of "white ghosts". But these changes are only in central.
Cheers, Bjoern
Still having a hard time and some strange situations. It is almost too much to report via email.
Basically, the tool_dependencies.xml get recognised sometimes. Please, watch this video to see what I mean (1'30''), and pause as you like: https://dl.dropboxusercontent.com/u/18352887/toolshedissues.ogv
I am afraid I cannot invest this amount of time to make my repo's public-proof. There are weird things happening which make no sense to me. And debugging of tool_dependencies.xml is very hard, since I find almost no logs of this process.
Joachim.
Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team
On 09/30/2013 02:53 PM, Dave Bouvier wrote:
Joachim,
For sourceforge URLs, you can safely omit the question mark and everything after it, since that's part of the browser download load balancing process. When downloading with wget, curl, or python's urllib, downloads.sourceforge.net does its own behind-the-scenes load balancing. As for hyphens, I don't believe they need to be escaped, since they're not XML entities like the ampersand is. The following download_by_url action should work:
<action type="download_by_url">http://downloads.sourceforge.net/project/transpose/transpose/transpose-2.0/2...</action>
--Dave B.On 09/30/2013 08:45 AM, Joachim Jacob | VIB | wrote:
Hi all,
Not fixed yet. Somehow the download does not work: I have escaped the ampersands and the hyphens. The download seems to have to proceed, since I receive no error from the download step. The next step in the dependencies file gives an error: mv: cannot stat transpose.zip': No such file or directory
Cheers, J
Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team
On 09/30/2013 02:06 PM, Peter Cock wrote:
You must escape any ampersand in the XML as & and then it should work.
Peter
On Mon, Sep 30, 2013 at 12:51 PM, Joachim Jacob | VIB | joachim.jacob@vib.be wrote:
Hi all,
The download URL seems not to be accepted in tool_dependencies.xml. It is an URL from sourceforge, the direct link to a package.
The error upon uploading the tool to my toolshed:
Metadata may have been defined for some items in revision '5665a799775d'. Correct the following problems if necessary and reset metadata. tool_dependencies.xml - Exception attempting to parse /mnt/toolsheddb/database/000/repo_26/tool_dependencies.xml: not well-formed (invalid token): line 6, column 149
The tool_dependencies.xml file:
1 <?xml version="1.0"?> 2 <tool_dependency> 3 <package name="transpose" version="2.0.0"> 4 <install version="1.0"> 5 <actions> 6 <action type="download_by_url">http://downloads.sourceforge.net/project/transpose/transpose/transpose-2.0/2...</action>
7 <action type="shell_command">mkdir bin</action> 8 <action type="shell_command">unzip transpose-2.0.zip</action> <action type="shell_command">cd transpose-2.0/src</action> <action type="shell_command">gcc transpose.c -o transpose</action> <action type="move_file">
<source>$INSTALL_DIR/transpose-2.0/src/transpose</source> <destination>$INSTALL_DIR/bin</destination> </action> <action type="shell_command">chmod +x $INSTALL_DIR/bin/transpose</action> <action type="set_environment"> <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> </action> </actions> </install> <readme> Compiling transpose and putting in the path. </readme> </package> </tool_dependency> **************
Cheers, Joachim
-- Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team
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/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
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/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Hi Joachim,
I don't think that is possible at the moment (its not a general problem, but in this cycle it seems to be). Currently I can not install from the test toolshed in my stable test branch. Because the tool shed is not forward compatible (yet). I can be wrong, but if you get an error, that is probably the reason. There is a trello card about forward compatibility, somewhere.
Ciao, Bjoern
Thanks, then I will run toolshed from a separate galaxy-central clone if that's advisable - different from the Galaxy service. I prefer to keep galaxy-dist on the stable branch.
In this process, I will move the tools from the old toolshed to my new toolshed running from galaxy-central. When I have time, I will upload everything to the test-toolshed.
Cheers, Joachim
Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team
On 09/30/2013 05:11 PM, Bjoern Gruening wrote:
Hi Joachim,
I had such problems if my XML file is invalid. Than I get immediately the 'installed:' text and can click install again, without any change. Also I would really recommend to reset your toolshed. These "white ghosts" can have unpredictable effects.
If you can upload your tools to the test tool shed I can try to install it debug it.
Please make sure that you run the latest Galaxy central version. Greg and Dave invested a lot of time to get rid of "white ghosts". But these changes are only in central.
Cheers, Bjoern
Still having a hard time and some strange situations. It is almost too much to report via email.
Basically, the tool_dependencies.xml get recognised sometimes. Please, watch this video to see what I mean (1'30''), and pause as you like: https://dl.dropboxusercontent.com/u/18352887/toolshedissues.ogv
I am afraid I cannot invest this amount of time to make my repo's public-proof. There are weird things happening which make no sense to me. And debugging of tool_dependencies.xml is very hard, since I find almost no logs of this process.
Joachim.
Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team
On 09/30/2013 02:53 PM, Dave Bouvier wrote:
Joachim,
For sourceforge URLs, you can safely omit the question mark and everything after it, since that's part of the browser download load balancing process. When downloading with wget, curl, or python's urllib, downloads.sourceforge.net does its own behind-the-scenes load balancing. As for hyphens, I don't believe they need to be escaped, since they're not XML entities like the ampersand is. The following download_by_url action should work:
<action type="download_by_url">http://downloads.sourceforge.net/project/transpose/transpose/transpose-2.0/2...</action>
--Dave B.On 09/30/2013 08:45 AM, Joachim Jacob | VIB | wrote:
Hi all,
Not fixed yet. Somehow the download does not work: I have escaped the ampersands and the hyphens. The download seems to have to proceed, since I receive no error from the download step. The next step in the dependencies file gives an error: mv: cannot stat transpose.zip': No such file or directory
Cheers, J
Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team
On 09/30/2013 02:06 PM, Peter Cock wrote:
You must escape any ampersand in the XML as & and then it should work.
Peter
On Mon, Sep 30, 2013 at 12:51 PM, Joachim Jacob | VIB | joachim.jacob@vib.be wrote: > Hi all, > > > The download URL seems not to be accepted in tool_dependencies.xml. > It is an > URL from sourceforge, the direct link to a package. > > The error upon uploading the tool to my toolshed: > ************** > Metadata may have been defined for some items in revision > '5665a799775d'. > Correct the following problems if necessary and reset metadata. > tool_dependencies.xml - Exception attempting to parse > /mnt/toolsheddb/database/000/repo_26/tool_dependencies.xml: not > well-formed > (invalid token): line 6, column 149 > ************** > > The tool_dependencies.xml file: > ************** > 1 <?xml version="1.0"?> > 2 <tool_dependency> > 3 <package name="transpose" version="2.0.0"> > 4 <install version="1.0"> > 5 <actions> > 6 <action > type="download_by_url">http://downloads.sourceforge.net/project/transpose/transpose/transpose-2.0/2...</action> > > > 7 <action type="shell_command">mkdir bin</action> > 8 <action type="shell_command">unzip > transpose-2.0.zip</action> > <action type="shell_command">cd > transpose-2.0/src</action> > <action type="shell_command">gcc transpose.c -o > transpose</action> > <action type="move_file"> > <source>$INSTALL_DIR/transpose-2.0/src/transpose</source> > <destination>$INSTALL_DIR/bin</destination> > </action> > <action type="shell_command">chmod +x > $INSTALL_DIR/bin/transpose</action> > <action type="set_environment"> > <environment_variable name="PATH" > action="prepend_to">$INSTALL_DIR/bin</environment_variable> > </action> > </actions> > </install> > <readme> > Compiling transpose and putting in the path. > </readme> > </package> > </tool_dependency> > ************** > > > Cheers, > Joachim > > -- > Joachim Jacob > Contact details: http://www.bits.vib.be/index.php/about/80-team > > > ___________________________________________________________ > 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/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/
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/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
OK, so toolshed running on galaxy-central is not an option. Then I need to remove the white ghosts by hand everytime they appear.
Cheers, Joachim
Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team
On 10/01/2013 09:39 AM, Bjoern Gruening wrote:
Hi Joachim,
I don't think that is possible at the moment (its not a general problem, but in this cycle it seems to be). Currently I can not install from the test toolshed in my stable test branch. Because the tool shed is not forward compatible (yet). I can be wrong, but if you get an error, that is probably the reason. There is a trello card about forward compatibility, somewhere.
Ciao, Bjoern
Thanks, then I will run toolshed from a separate galaxy-central clone if that's advisable - different from the Galaxy service. I prefer to keep galaxy-dist on the stable branch.
In this process, I will move the tools from the old toolshed to my new toolshed running from galaxy-central. When I have time, I will upload everything to the test-toolshed.
Cheers, Joachim
Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team
On 09/30/2013 05:11 PM, Bjoern Gruening wrote:
Hi Joachim,
I had such problems if my XML file is invalid. Than I get immediately the 'installed:' text and can click install again, without any change. Also I would really recommend to reset your toolshed. These "white ghosts" can have unpredictable effects.
If you can upload your tools to the test tool shed I can try to install it debug it.
Please make sure that you run the latest Galaxy central version. Greg and Dave invested a lot of time to get rid of "white ghosts". But these changes are only in central.
Cheers, Bjoern
Still having a hard time and some strange situations. It is almost too much to report via email.
Basically, the tool_dependencies.xml get recognised sometimes. Please, watch this video to see what I mean (1'30''), and pause as you like: https://dl.dropboxusercontent.com/u/18352887/toolshedissues.ogv
I am afraid I cannot invest this amount of time to make my repo's public-proof. There are weird things happening which make no sense to me. And debugging of tool_dependencies.xml is very hard, since I find almost no logs of this process.
Joachim.
Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team
On 09/30/2013 02:53 PM, Dave Bouvier wrote:
Joachim,
For sourceforge URLs, you can safely omit the question mark and everything after it, since that's part of the browser download load balancing process. When downloading with wget, curl, or python's urllib, downloads.sourceforge.net does its own behind-the-scenes load balancing. As for hyphens, I don't believe they need to be escaped, since they're not XML entities like the ampersand is. The following download_by_url action should work:
<action type="download_by_url">http://downloads.sourceforge.net/project/transpose/transpose/transpose-2.0/2...</action>
--Dave B.On 09/30/2013 08:45 AM, Joachim Jacob | VIB | wrote:
Hi all,
Not fixed yet. Somehow the download does not work: I have escaped the ampersands and the hyphens. The download seems to have to proceed, since I receive no error from the download step. The next step in the dependencies file gives an error: mv: cannot stat transpose.zip': No such file or directory
Cheers, J
Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team
On 09/30/2013 02:06 PM, Peter Cock wrote: > You must escape any ampersand in the XML as & and then it should > work. > > Peter > > On Mon, Sep 30, 2013 at 12:51 PM, Joachim Jacob | VIB | > joachim.jacob@vib.be wrote: >> Hi all, >> >> >> The download URL seems not to be accepted in tool_dependencies.xml. >> It is an >> URL from sourceforge, the direct link to a package. >> >> The error upon uploading the tool to my toolshed: >> ************** >> Metadata may have been defined for some items in revision >> '5665a799775d'. >> Correct the following problems if necessary and reset metadata. >> tool_dependencies.xml - Exception attempting to parse >> /mnt/toolsheddb/database/000/repo_26/tool_dependencies.xml: not >> well-formed >> (invalid token): line 6, column 149 >> ************** >> >> The tool_dependencies.xml file: >> ************** >> 1 <?xml version="1.0"?> >> 2 <tool_dependency> >> 3 <package name="transpose" version="2.0.0"> >> 4 <install version="1.0"> >> 5 <actions> >> 6 <action >> type="download_by_url">http://downloads.sourceforge.net/project/transpose/transpose/transpose-2.0/2...</action> >> >> >> 7 <action type="shell_command">mkdir bin</action> >> 8 <action type="shell_command">unzip >> transpose-2.0.zip</action> >> <action type="shell_command">cd >> transpose-2.0/src</action> >> <action type="shell_command">gcc transpose.c -o >> transpose</action> >> <action type="move_file"> >> <source>$INSTALL_DIR/transpose-2.0/src/transpose</source> >> <destination>$INSTALL_DIR/bin</destination> >> </action> >> <action type="shell_command">chmod +x >> $INSTALL_DIR/bin/transpose</action> >> <action type="set_environment"> >> <environment_variable name="PATH" >> action="prepend_to">$INSTALL_DIR/bin</environment_variable> >> </action> >> </actions> >> </install> >> <readme> >> Compiling transpose and putting in the path. >> </readme> >> </package> >> </tool_dependency> >> ************** >> >> >> Cheers, >> Joachim >> >> -- >> Joachim Jacob >> Contact details: http://www.bits.vib.be/index.php/about/80-team >> >> >> ___________________________________________________________ >> 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/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ ___________________________________________________________ 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/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
galaxy-dev@lists.galaxyproject.org
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Bjoern Gruening -
Dave Bouvier -
Joachim Jacob | VIB | -
Nicola Soranzo -
Peter Cock