On Tue, Apr 17, 2012 at 1:00 PM, JIE CHEN jiechenable1987@gmail.com wrote:
Thank you Nate. Your advise is very helpful to me. I installed the binaries like you said. Right now the binaries can be run successfully in the command line prompt. However i run into other problems :
Failed to open input file: /usr/local/projects/galaxy-dist/tool-data/taxonomy/names.dmp
What i have done:
- downloaded the .tar.gz file from the link you told me
- tar zxvf name.tar.gz
- then i found the three executables which are: taxBuilder, taxonomy2tree
and tree2PS-fast. 4. made symbolic link of these files to the /usr/local/bin
what else shall i do? Thanks.
Tyler
On Tue, Apr 17, 2012 at 10:36 AM, Nate Coraor nate@bx.psu.edu wrote:
On Apr 17, 2012, at 1:32 PM, JIE CHEN wrote:
Dear all,
I was trying to run the build-in function "Fetch taxonomic
representation" on my local instance of Galaxy, however it doesn't work as I expect.
The error message is: /bin/sh: taxBuilder: not found
Anyone has seen this problem before? Please tell me what to do to solve
this problem? A lot of thanks
Hi Tyler,
Some Galaxy tools depend on external binaries not included in the Galaxy distribution, and this is one of those tools. The full list and where to get the tools from can be found here:
http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Dependencies
This specific tool can be found at:
https://bitbucket.org/natefoo/taxonomy
--nate
Tyler ___________________________________________________________ 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:
--- 12年4月18日，周三, JIE CHEN jiechenable1987@gmail.com 写道：
发件人: JIE CHEN jiechenable1987@gmail.com 主题: Re: [galaxy-dev] "Fetch taxonomic representation" DOESN'T WORK 收件人: galaxy-dev@lists.bx.psu.edu 日期: 2012年4月18日,周三,上午5:36
On Tue, Apr 17, 2012 at 1:00 PM, JIE CHEN jiechenable1987@gmail.com wrote:
Thank you Nate. Your advise is very helpful to me. I installed the binaries like you said. Right now the binaries can be run successfully in the command line prompt. However i run into other problems : Failed to open input file: /usr/local/projects/galaxy-dist/tool-data/taxonomy/names.dmp
What i have done: 1. downloaded the .tar.gz file from the link you told me 2. tar zxvf name.tar.gz 3. then i found the three executables which are: taxBuilder, taxonomy2tree and tree2PS-fast. 4. made symbolic link of these files to the /usr/local/bin
what else shall i do? Thanks.
Tyler
The file may not exist. To generate the dependent files, you can try the following steps (change the path to yours):
Go to /mnt/galaxyTools/galaxy-central/scripts/taxonomy Run processTaxonomy.sh, which will generate the file gi_taxid_sorted.txt and other files. Link those files to the directory /mnt/galaxyTools/galaxy-central/tool-data/taxonomy mkdir /mnt/galaxyTools/galaxy-central/tool-data/taxonomy ls|awk '{print "ln -s /mnt/galaxyIndices/AdditionalData/taxonomy/"$1" /mnt/galaxyTools/galaxy-central/tool-data/taxonomy/"$1}'|sh zhengqiu cai
On Tue, Apr 17, 2012 at 10:36 AM, Nate Coraor nate@bx.psu.edu wrote:
On Apr 17, 2012, at 1:32 PM, JIE CHEN wrote:
Dear all,
I was trying to run the build-in function "Fetch taxonomic representation" on my local instance of Galaxy, however it doesn't work as I expect. The error message is: /bin/sh: taxBuilder: not found
Anyone has seen this problem before? Please tell me what to do to solve this problem? A lot of thanks
Hi Tyler,
Some Galaxy tools depend on external binaries not included in the Galaxy distribution, and this is one of those tools. The full list and where to get the tools from can be found here:
http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Dependencies
This specific tool can be found at:
https://bitbucket.org/natefoo/taxonomy
--nate
Tyler ___________________________________________________________ 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:
-----下面为附件内容-----
___________________________________________________________ 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:
--- 12年4月18日，周三, zhengqiu cai caizhq2005@yahoo.com.cn 写道：
发件人: zhengqiu cai caizhq2005@yahoo.com.cn 主题: Re: [galaxy-dev] "Fetch taxonomic representation" DOESN'T WORK 收件人: galaxy-dev@lists.bx.psu.edu, "JIE CHEN" jiechenable1987@gmail.com 日期: 2012年4月18日,周三,下午10:58
--- 12年4月18日，周三, JIE CHEN jiechenable1987@gmail.com 写道：
发件人: JIE CHEN jiechenable1987@gmail.com 主题: Re: [galaxy-dev] "Fetch taxonomic representation" DOESN'T WORK 收件人: galaxy-dev@lists.bx.psu.edu 日期: 2012年4月18日,周三,上午5:36
On Tue, Apr 17, 2012 at 1:00 PM, JIE CHEN jiechenable1987@gmail.com wrote:
Thank you Nate. Your advise is very helpful to me. I installed the binaries like you said. Right now the binaries can be run successfully in the command line prompt. However i run into other problems : Failed to open input file: /usr/local/projects/galaxy-dist/tool-data/taxonomy/names.dmp
What i have done: 1. downloaded the .tar.gz file from the link you told me 2. tar zxvf name.tar.gz 3. then i found the three executables which are: taxBuilder, taxonomy2tree and tree2PS-fast. 4. made symbolic link of these files to the /usr/local/bin
what else shall i do? Thanks.
Tyler
The file may not exist. To generate the dependent files, you can try the following steps (change the path to yours):
Go to /mnt/galaxyTools/galaxy-central/scripts/taxonomy Run processTaxonomy.sh, which will generate the file gi_taxid_sorted.txt and other files. Link those files to the directory /mnt/galaxyTools/galaxy-central/tool-data/taxonomy mkdir /mnt/galaxyTools/galaxy-central/tool-data/taxonomy ls|awk '{print "ln -s /mnt/galaxyIndices/AdditionalData/taxonomy/"$1" /mnt/galaxyTools/galaxy-central/tool-data/taxonomy/"$1}'|sh Sorry, it should be: ls|awk '{print "ln -s /mnt/galaxyTools/galaxy-central/scripts/taxonomy/"$1" /mnt/galaxyTools/galaxy-central/tool-data/taxonomy/"$1}'|sh or you can copy the directory /mnt/galaxyTools/galaxy-central/scripts/taxonomy to /mnt/galaxyTools/galaxy-central/tool-data/taxonomy zhengqiu cai
On Tue, Apr 17, 2012 at 10:36 AM, Nate Coraor nate@bx.psu.edu wrote:
On Apr 17, 2012, at 1:32 PM, JIE CHEN wrote:
Dear all,
I was trying to run the build-in function "Fetch taxonomic representation" on my local instance of Galaxy, however it doesn't work as I expect. The error message is: /bin/sh: taxBuilder: not found
Anyone has seen this problem before? Please tell me what to do to solve this problem? A lot of thanks
Hi Tyler,
Some Galaxy tools depend on external binaries not included in the Galaxy distribution, and this is one of those tools. The full list and where to get the tools from can be found here:
http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Dependencies
This specific tool can be found at:
https://bitbucket.org/natefoo/taxonomy
--nate
Tyler ___________________________________________________________ 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:
-----下面为附件内容-----
___________________________________________________________ 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:
-----下面为附件内容-----
___________________________________________________________ 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
-
JIE CHEN -
zhengqiu cai