Question: Blast sequence using bacterial genome of ncbi
0
gravatar for cbb.chintan
3.2 years ago by
cbb.chintan10
United States
cbb.chintan10 wrote:

Hello,

I have installed my galaxy on local server and successfully and added NCBI BLAST plus. I want to blast my nucleotide sequence with bacteria genome for getting protein sequences (tBlastn or Blastx). But when I try,  it shown there is no Reference NCBI blast genome available.

 

Best,

Chintan

genome ncbi bacterial blastp • 1.2k views
ADD COMMENTlink modified 3.2 years ago by Jennifer Hillman Jackson25k • written 3.2 years ago by cbb.chintan10
0
gravatar for Jennifer Hillman Jackson
3.2 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

You will need to add in the databases. There is no Data Manager available yet for this function, so you could write one using the existing repos in the Tool Shed as examples. Or, you can add in the data directly following the instructions in the Blast+ ReadMe document: https://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus/577d9c12411a

Take care, Jen, Galaxy team

ADD COMMENTlink written 3.2 years ago by Jennifer Hillman Jackson25k

Thank you for your reply.

As you suggested me to go to link in previous mail I did the same procedure and installed ncbi_blast_plus using tool shed. Then, i tried to download both Dependencies of this repository, [1] blast datatypes, [2]"package_blast_plus_2_2_31" as required by tool.

I am able to download and install first dependency, blast datatypes. Second dependency, package_blast_plus_2_2_31, this required to download blast+ [version 2.2.31]. When i tried to install this, it shows following message "Set the value of your tool_dependency_dir setting in your Galaxy config file (galaxy.ini) and restart your Galaxy server to install tool dependencies".

Secondly, i search and did as i got some clues, added tool_dependency_dir = dependency_dir in galaxy.ini file, and then restarted galaxy but getting same message.

I hope you can help as i am very near to my point.

You can find attachment.... Best, Chintan

ADD REPLYlink written 3.2 years ago by cbb.chintan10

Hello,

I am able to download blast+ package after removing "#" this from tool_dependency_dir = dependency_dir in galaxy.ini file. But, again i am facing another problem. When i try to install this i got following message.

File "/home/qiime/galaxy/lib/tool_shed/galaxy_install/install_manager.py", line 136, in install_and_build_package_via_fabric tool_dependency = self.install_and_build_package( install_environment, tool_shed_repository, tool_dependency, actions_dict ) File "/home/qiime/galaxy/lib/tool_shed/galaxy_install/install_manager.py", line 121, in install_and_build_package initial_download=False ) File "/home/qiime/galaxy/lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py", line 32, in execute_step initial_download=initial_download ) File "/home/qiime/galaxy/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", line 1798, in execute_step return_output=False ) File "/home/qiime/galaxy/lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py", line 126, in handle_command output = self.handle_complex_command( command ) File "/home/qiime/galaxy/lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py", line 166, in handle_complex_command cwd=state.env[ 'lcwd' ] ) File "/home/qiime/qiime_software/python-2.7.3-release/lib/python2.7/subprocess.py", line 679, in init errread, errwrite) File "/home/qiime/qiime_software/python-2.7.3-release/lib/python2.7/subprocess.py", line 1249, in _execute_child raise child_exception [Errno 2] No such file or directory: '/home/qiime/galaxy/database/tmp/tmp-toolshed-mtdFAQR8W/blast+'Installed tool dependencies: blast+

I am not understanding, why this happen?

Best, Chintan

ADD REPLYlink written 3.2 years ago by cbb.chintan10
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