Friday, April 28, 2017

command line - How do I make Xmipp (Image processing software) work on Ubuntu 16.04.01?

I am new to Ubuntu and I am currently running it on Oracle VM VirtualBox in order to work with a software called Xmipp (more details about the software on http://xmipp.cnb.csic.es/twiki/bin/view/Xmipp/WebHome).



Now, I followed the HowToInstall guide, which first requires me to download the Linux Binaries(Ubuntu) from this link. And then, as mentioned on the HowToInstall link, I chose




Option 1:Using Precompiled Binaries





and executed the install_binaries.sh script. I then go the following message:



> #!/bin/bash ID=$$ cat .xmipp.bashrc |grep XMIPP_HOME= |cut -d "=" -f 1 |sed -e "s/XMIPP_HOME/XMIPP_HOME=$(pwd | sed -e 's/\//\\\//g')/g" >
> /tmp/xmipp_binary_creating_${ID} && cat $(pwd)/.xmipp.bashrc |egrep -v
> ".xmipp.cfg|XMIPP_HOME=|^#" >> /tmp/xmipp_binary_creating_${ID} &&
> echo "test -s $(pwd)/.xmipp.cfg && . $(pwd)/.xmipp.cfg || true" >>
> /tmp/xmipp_binary_creating_${ID} && mv
> /tmp/xmipp_binary_creating_${ID} $(pwd)/.xmipp.bashrc && source

> $(pwd)/.xmipp.bashrc && echo 'Xmipp3.0 binaries have been succesfully
> installed in your system. Please, put a source to .xmipp.bashrc file
> in your .bashrc file. Just for this session, .xmipp.bashrc has been
> already sourced, so if you executed the install_binaries.sh script
> with source or . changes will be applied to this shell and so, you
> should be able to execute xmipp from this terminal. If you did it with
> ./install_binaries.sh its time to source .xmipp.bashrc manually to
> have xmipp working in this shell session.'



Since the message says that Xmipp 3.0 Binaries are installed, I then went on to this link and followed the instructions mentioned under




Running library tests (optional but recommended)




Now this is the part where I am finding it difficult to follow the instructions because the authors mention that




you can run the tests by executing (from inside Xmipp home directory)

the command:




xcompile gtest=yes run_tests


Now I downloaded Xmipp 3.0 as a file with the following name Xmipp-3.1-linuxbin-all-x86_64.tar.gz and extracted it to my desktop. Therefore, I went to the terminal and wrote



cd ~/Desktop/xcompile gtest=yes run_tests



But then I go at error saying bash: cd: /home/shrey/Desktop/xcompile: No such file or directory. Could please explain what am I doing wrong and how can I make Xmipp work on Ubuntu.

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