Problem with installation of blaSTorage

Use this forum for general bioinformatics questions, or questions regarding genomics, proteomics, etc.

Moderators: mdfenko, Abhijeet Bakre, strom

Problem with installation of blaSTorage

Postby Morgis89 » Mar 29 2016 3:35 pm

Hey

I have a problem with installation of blaSTorage on my ubuntu. I have a many results from standalone psiblast and i read that the new blast writing results in xml and using Biopython for parse many sequences is problematic. So i was looking for something else and found that package http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3571973/
But the instalation is a problem becouse im not an ace in linux and the instalation file is not tar.gz as author said no more. Its zip. Seriously stupid problem but please, can someone help?

Or can someone reccomend an alternative way?

Also Im using Anaconda2.

Regards
M
Morgis89
newcomer
newcomer
 
Posts: 3
Joined: Nov 12 2015 11:21 pm

Re: Problem with installation of blaSTorage

Postby r.rosati » Mar 29 2016 7:20 pm

You are correct. What flavor of linux are you using?
In Ubuntu, you'd need the unzip module:
Code: Select all
sudo apt-get install unzip


You'd navigate to the location you have blastorage in (move it if you wish), and then:
Code: Select all
unzip blastorage.zip

or if you wish,
Code: Select all
unzip blastorage.zip -d destination_folder


This would substitute the
Code: Select all
tar zxvf blastorage.tar.gz
line in the manual.
r.rosati
ModSquad
ModSquad
 
Posts: 2154
Joined: Nov 04 2002 3:23 pm
Location: Brazil

Re: Problem with installation of blaSTorage

Postby Morgis89 » Mar 31 2016 12:38 pm

Hey, tkank you for help.
I didnt know how to install python module (Im truly beginner :) )

here what ive do:

1. unziped this file
2. in terminal cd to this folder where files was unziped
3. in terminal typed "python setup install" setup file -> from unziped files
4. check that module exist for python and can be imported (in my case in spyder, but it doesnt matter. it can be just python interpreter)

realy light-hearted problem

Regards
:roll:
Morgis89
newcomer
newcomer
 
Posts: 3
Joined: Nov 12 2015 11:21 pm

Re: Problem with installation of blaSTorage

Postby r.rosati » Mar 31 2016 2:32 pm

It should have worked - just, the setup file will not be directly in the folder where you unzipped everything, you need to `cd` further to the unzipped `blastorage` folder that's inside it.
There you should find the setup file, and can now use python to open it with `python setup install`.
Did it work then?
Best!
Roberto
r.rosati
ModSquad
ModSquad
 
Posts: 2154
Joined: Nov 04 2002 3:23 pm
Location: Brazil


Return to General Bioinformatics

Who is online

Users browsing this forum: No registered users and 3 guests

cron