Toolshed tool_dependency.xml git archive configure issue
Hi folks, Having a difficult time with coding the "configure" step in this new tool_dependency.xml file, namely that an error "/bin/sh: configure: command not found" results when I try to install my beta development tool from a local test toolshed (which is downloading and installing other tools just fine). <actions> <action type="shell_command">git clone https://github.com/myuser/mygitstuff.git .</action> <action type="shell_command">git reset --hard 1819482db93bf0025c2588b5264cc0ec8c61029c</action> <action type="shell_command">configure --disable-gui --prefix=$INSTALL_DIR</action> <action type="make_install"></action> <action type="move_directory_files"> <source_directory>bin</source_directory> <destination_directory>$INSTALL_DIR/bin</destination_directory> </action> <action type="set_environment"> <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> </action> </actions> Any hints about why this isn't being found or what the /bin/sh needs to get it going? When I do a git reset --hard, the "configure" file is definitely there, with executable flag set. Any other permission oddities? I've also tried <action type="autoconf"></action> , which yeilds same error. (Skipping that line and doing <action type="make_install"></action> at least finds and runs "make", though it errors out for lack of input data). Regards, Damion Hsiao lab, BC Public Health Microbiology & Reference Laboratory, BC Centre for Disease Control 655 West 12th Avenue, Vancouver, British Columbia, V5Z 4R4 Canada
Hey Damion, You should be able to do *./*configure --disable-gui ... to get it to work (that is, make sure the full path to the configure command is given). At least I think that's probably what's going on. Aaron On Fri, Aug 1, 2014 at 12:32 PM, Dooley, Damion <Damion.Dooley@bccdc.ca> wrote:
Hi folks,
Having a difficult time with coding the "configure" step in this new tool_dependency.xml file, namely that an error "/bin/sh: configure: command not found" results when I try to install my beta development tool from a local test toolshed (which is downloading and installing other tools just fine).
<actions> <action type="shell_command">git clone https://github.com/myuser/mygitstuff.git .</action> <action type="shell_command">git reset --hard 1819482db93bf0025c2588b5264cc0ec8c61029c</action> <action type="shell_command">configure --disable-gui --prefix=$INSTALL_DIR</action> <action type="make_install"></action> <action type="move_directory_files"> <source_directory>bin</source_directory>
<destination_directory>$INSTALL_DIR/bin</destination_directory> </action> <action type="set_environment"> <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> </action> </actions>
Any hints about why this isn't being found or what the /bin/sh needs to get it going? When I do a git reset --hard, the "configure" file is definitely there, with executable flag set. Any other permission oddities?
I've also tried <action type="autoconf"></action> , which yeilds same error. (Skipping that line and doing <action type="make_install"></action> at least finds and runs "make", though it errors out for lack of input data).
Regards,
Damion
Hsiao lab, BC Public Health Microbiology & Reference Laboratory, BC Centre for Disease Control 655 West 12th Avenue, Vancouver, British Columbia, V5Z 4R4 Canada
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Sadly, <action type="shell_command">./configure --disable-gui --prefix=$INSTALL_DIR</action> yeilds install error: /bin/sh: ./configure: No such file or directory But file must be there since previous git step is carried out ok: ... ############################################# git reset --hard 1819482db93bf0025c2588b5264cc0ec8c61029c STDOUT HEAD is now at 1819482 Added gitignore ############################################# git reset --hard 1819482db93bf0025c2588b5264cc0ec8c61029c STDERR ############################################# ./configure --disable-gui --prefix=/usr/local/galaxy/shared/tool_dependency/ffp-phylogeny/0.3.19_1819482db93bf0025c2588b5264cc0ec8c61029c/ddooley/ffp_phylogeny/4e213eee0fef STDOUT ############################################# ./configure --disable-gui --prefix=/usr/local/galaxy/shared/tool_dependency/ffp-phylogeny/0.3.19_1819482db93bf0025c2588b5264cc0ec8c61029c/ddooley/ffp_phylogeny/4e213eee0fef STDERR /bin/sh: ./configure: No such file or directory ############################################# argh! d. ________________________________________ From: Aaron Petkau [aaron.petkau@gmail.com] Sent: Friday, August 01, 2014 11:47 AM To: Dooley, Damion Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Toolshed tool_dependency.xml git archive configure issue Hey Damion, You should be able to do ./configure --disable-gui ... to get it to work (that is, make sure the full path to the configure command is given). At least I think that's probably what's going on. Aaron
A little more info: <action type="shell_command">ls -a</action> ############################################# ls -a STDOUT . .. ############################################# ############################################# ls -a STDERR so I guess the .git archive is being unpackaged somewhere else! After lunch I'll return to explore this mysterious territory. d.
Hmmm... you know what. I tested this out and it looks like Galaxy expects the git repo to be named the same as the package name in your tool dependencies file ffp-phylogeny. If you change the git command to: git clone https://github.com/apetkau/ffp-3.19-custom.git *ffp-phylogeny* I think it should work. Aaron On Fri, Aug 1, 2014 at 2:09 PM, Dooley, Damion <Damion.Dooley@bccdc.ca> wrote:
A little more info:
<action type="shell_command">ls -a</action>
############################################# ls -a STDOUT . .. #############################################
############################################# ls -a STDERR
so I guess the .git archive is being unpackaged somewhere else! After lunch I'll return to explore this mysterious territory.
d.
That was it! Yay! I'll add a Trello card to have this info gem added to the docs. Thanks, Damion Hsiao lab, BC Public Health Microbiology & Reference Laboratory, BC Centre for Disease Control 655 West 12th Avenue, Vancouver, British Columbia, V5Z 4R4 Canada ________________________________________ From: Aaron Petkau [aaron.petkau@gmail.com] Sent: Friday, August 01, 2014 12:26 PM To: Dooley, Damion Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Toolshed tool_dependency.xml git archive configure issue Hmmm... you know what. I tested this out and it looks like Galaxy expects the git repo to be named the same as the package name in your tool dependencies file ffp-phylogeny. If you change the git command to: git clone https://github.com/apetkau/ffp-3.19-custom.git ffp-phylogeny I think it should work. Aaron
participants (2)
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Aaron Petkau -
Dooley, Damion