<div dir="ltr"><div>Hello mrtrixers.<br><br></div>The issue of running mrtrix on a non-debian OS has come up before in this list. As we have access to a moderately large cluster that we want to use but that unfortunately does not run a debian flavor, we had to do something about it. <br>
<div><div><div><br></div><div>The always up to date instructions are <a href="https://docs.google.com/document/d/1b1d--oSQXb29FVPZFpwD1Wuj0nIDUK1allN4ceXoOSc/edit?usp=sharing">here</a>:<br><a href="https://docs.google.com/document/d/1b1d--oSQXb29FVPZFpwD1Wuj0nIDUK1allN4ceXoOSc/edit?usp=sharing">https://docs.google.com/document/d/1b1d--oSQXb29FVPZFpwD1Wuj0nIDUK1allN4ceXoOSc/edit?usp=sharing</a><br>
<br></div><div>and are copied below as a reference to the list users. While it is not immediately user-friendly, it is not as hard once all dependencies are met. It is working like a charm for us, and it sure beats having to replace the OS on the computing cluster!<br>
<br></div><div>Full credit and kudos go to Edgar Morales, who configured and documented all of this work. I hope this ensures that no mrtrixer is left behind due to an OS incompatibility.<br></div><div><br></div><div>Cheers!<br>
<br>Dr. Luis Concha<br>Instituto de Neurobiología<br>Laboratorio C-13<br>UNAM, Campus Juriquilla<br>Boulervard Juriquilla 3001<br>Juriquilla, Querétaro.<br>C.P. 76230<br>México<br>Tel (442) 2 38 10 54<br>Fax (442) 2 38 10 46<br>
<a href="http://www.inb.unam.mx" target="_blank">www.inb.unam.mx</a><br></div><div><br><br><br><br>-------------------------------------------------------------<br></div><div>Begin instructions<br></div><div>--------------------------------------------------------------<br>
<p dir="ltr" style="line-height:1.15;margin-top:0pt;margin-bottom:0pt" id="docs-internal-guid-442b2180-30ba-6f37-0e59-26db99a40e87"><span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline">The problem of dependences for mrtrix in CentOS 5.2 can be solved using schroot with a debian distribution that has the possibility to use the neurodebian repositories. The approximation that resulted best for us, was to compile all the programs that are needed in a virtual machine with CentOS 5.2, specifically we use virtualbox to virtualize the operative system. </span></p>
<p dir="ltr" style="line-height:1.15;margin-top:0pt;margin-bottom:0pt"><span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline">First we compile schroot, so we need to download the schroot-1.1.5-4.src.rpm source package from <a href="http://www.nikhef.nl/~dennisvd/schroot.html">http://www.nikhef.nl/~dennisvd/schroot.html</a>. </span></p>
<p dir="ltr" style="line-height:1.15;margin-top:0pt;margin-bottom:0pt"><span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline">In CentOS is necessary to install this libraries:</span></p>
<h3 dir="ltr" style="line-height:1.15;margin-top:8pt;margin-bottom:0pt"><span style="font-size:15px;font-family:'Courier New';color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline">yum install rpmbuild boost boost-devel pam-devel e2fsprogs-devel lock-devel gcc-c++ make lockdev-devel gcc kernel-devel</span></h3>
<h3 dir="ltr" style="line-height:1.15;margin-top:8pt;margin-bottom:0pt"><span style="font-size:15px;font-family:'Courier New';color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline">yum groupinstall “Development Tools” </span></h3>
<br><span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline"></span><p dir="ltr" style="line-height:1.15;margin-top:0pt;margin-bottom:0pt">
<span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline">Then we need to install the schroot package</span></p>
<h3 dir="ltr" style="line-height:1.15;margin-top:8pt;margin-bottom:0pt"><span style="font-size:15px;font-family:'Courier New';color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline">rpm -i schroot-1.1.5-4.src.rpm</span></h3>
<br><span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline"></span><p dir="ltr" style="line-height:1.15;margin-top:0pt;margin-bottom:0pt">
<span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline">At this point there was a problem with the installation, which we solved it with the creation of the </span><span style="font-size:15px;font-family:'Courier New';color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline">redhat</span><span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline"> directory in </span><span style="font-size:15px;font-family:'Courier New';color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline">/usr/src/ </span><span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline">but google found yet another solution which was not tested by us. The solution mentioned the use of the option nomd5</span></p>
<h3 dir="ltr" style="line-height:1.15;margin-top:8pt;margin-bottom:0pt"><span style="font-size:15px;font-family:'Courier New';color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline">rpm --nomd5 -i schroot-1.1.5-4.src.rpm</span></h3>
<br><span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline"></span><p dir="ltr" style="line-height:1.15;margin-top:0pt;margin-bottom:0pt">
<span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline">After the source is install is necessary change directory to SPECS inside the redhat directory and compile schroot:</span></p>
<br><span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline"></span><p dir="ltr" style="line-height:1.15;margin-top:0pt;margin-bottom:0pt">
<span style="font-size:15px;font-family:'Courier New';color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline">cd /usr/src/redhat/SPECS</span></p>
<p dir="ltr" style="line-height:1.15;margin-top:0pt;margin-bottom:0pt"><span style="font-size:15px;font-family:'Courier New';color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline">rpmbuild -bb schroot.spec</span></p>
<br><span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline"></span><br><span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline"></span><p dir="ltr" style="line-height:1.15;margin-top:0pt;margin-bottom:0pt">
<span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline">Then in the build directory we can find the schroot rpm package and the last step is to install it</span></p>
<br><span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline"></span><h3 dir="ltr" style="line-height:1.15;margin-top:8pt;margin-bottom:0pt">
<span style="font-size:15px;font-family:'Courier New';color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline">rpm -Uvh schroot-1.1.5-4.x86_64.rpm </span></h3>
<br><span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline"></span><p dir="ltr" style="line-height:1.15;margin-top:0pt;margin-bottom:0pt">
<span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline">The program debootstrap was downloaded from <a href="http://pkgs.org/centos-5-rhel-5/epel-i386/debootstrap-1.0.7-3.el5.noarch.rpm.html">http://pkgs.org/centos-5-rhel-5/epel-i386/debootstrap-1.0.7-3.el5.noarch.rpm.html</a></span></p>
<p dir="ltr" style="line-height:1.15;margin-top:0pt;margin-bottom:0pt"><span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline"> and the installation was straightforward</span></p>
<h3 dir="ltr" style="line-height:1.15;margin-top:8pt;margin-bottom:0pt"><span style="font-size:15px;font-family:'Courier New';color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline">rpm -Uvh debootstrap-1.0.7-3.el5.noarch.rpm</span></h3>
<br><span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline"></span><p dir="ltr" style="line-height:1.15;margin-top:0pt;margin-bottom:0pt">
<span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline">After this step we create a directory for the chroot and use debootstrap to download the chroot. Is important to notice that the </span><span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:italic;font-variant:normal;text-decoration:none;vertical-align:baseline">lenny</span><span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline"> distribution worked perfectly by using the archive repositories of debian. However, in order to install squeeze and have a newer version of mrtrix, it is necessary to create a symbolic link for squeeze in the </span><span style="font-size:15px;font-family:Arial;color:rgb(34,34,34);background-color:rgb(255,255,255);font-weight:normal;font-style:italic;font-variant:normal;text-decoration:none;vertical-align:baseline">/usr/lib/debootstrap/scripts </span></p>
<br><span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline"></span><p dir="ltr" style="line-height:1.15;margin-top:0pt;margin-bottom:0pt">
<span style="font-size:15px;font-family:'Courier New';color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline">ln -s </span><span style="font-size:15px;font-family:'Courier New';color:rgb(34,34,34);background-color:rgb(255,255,255);font-weight:normal;font-style:italic;font-variant:normal;text-decoration:none;vertical-align:baseline">/usr/lib/debootstrap/scripts/sid /usr/lib/debootstrap/scripts/squeeze</span><span style="font-size:15px;font-family:'Courier New';color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline"></span></p>
<br><span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline"></span><br><span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline"></span><p dir="ltr" style="line-height:1.15;margin-top:0pt;margin-bottom:0pt">
<span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline">Using debootstrap to install chroot we download the entire operating system. This command installs the OS in the directory that we recently create. </span></p>
<p dir="ltr" style="line-height:1.15;margin-top:0pt;margin-bottom:0pt"><span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline"> </span></p>
<p dir="ltr" style="line-height:1.15;margin-top:0pt;margin-bottom:0pt"><span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline">For Lenny:</span></p>
<p dir="ltr" style="line-height:1.15;margin-top:0pt;margin-bottom:0pt"><span style="font-size:15px;font-family:'Courier New';color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline">debotstrap --arch amd64 lenny lenny/ <a href="http://archive.debian.org/debian">http://archive.debian.org/debian</a></span></p>
<br><span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline"></span><p dir="ltr" style="line-height:1.15;margin-top:0pt;margin-bottom:0pt">
<span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline">For Squeeze:</span></p><br>
<span style="font-size:15px;font-family:'Courier New';color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline"></span><p dir="ltr" style="line-height:1.15;margin-top:0pt;margin-bottom:0pt">
<span style="font-size:15px;font-family:'Courier New';color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline">debotstrap --arch amd64 squeeze squeeze/ <a href="http://ftp.us.debian.org/debian">http://ftp.us.debian.org/debian</a></span></p>
<br><span style="font-size:15px;font-family:'Courier New';color:rgb(0,0,0);background-color:rgb(245,246,247);font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline"></span><p dir="ltr" style="line-height:1.15;margin-top:0pt;margin-bottom:0pt">
<span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline">Now we can modify the /etc/schroot/schroot.conf in order to include the chroot recently installed.</span></p>
<br><span style="font-size:15px;font-family:'Courier New';color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline"></span><p dir="ltr" style="line-height:1.15;margin-top:0pt;margin-bottom:0pt">
<span style="font-size:15px;font-family:'Courier New';color:rgb(0,0,0);background-color:rgb(255,255,255);font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline">[lenny]<br class="">
description=Debian Lenny<br class="">type=directory<br class="">location=/home/user/lenny<br class="">priority=3<br class="">users=YOUR_USER<br class="">groups=SOME_GROUP_LIKE_users<br class="">root-groups=YOUR_ADMIN_USER<br class="">
run-setup-scripts=true<br class="">run-exec-scripts=true</span></p><br><span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline"></span><p dir="ltr" style="line-height:1.15;margin-top:0pt;margin-bottom:0pt">
<span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline">In order to have internet acces is necesary to copy /etc/resolv.conf to the etc of the chroot something like:</span></p>
<br><span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline"></span><p dir="ltr" style="line-height:1.15;margin-top:0pt;margin-bottom:0pt">
<span style="font-size:15px;font-family:'Courier New';color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline">cp /etc/resolv.conf /home/user/lenny/etc/</span></p>
<br><span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline"></span><p dir="ltr" style="line-height:1.15;margin-top:0pt;margin-bottom:0pt">
<span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline">To get inside chroot we need to use the command :</span></p>
<br><span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline"></span><p dir="ltr" style="line-height:1.15;margin-top:0pt;margin-bottom:0pt">
<span style="font-size:15px;font-family:'Courier New';color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline">schroot -c lenny</span></p>
<br><span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline"></span><p dir="ltr" style="line-height:1.15;margin-top:0pt;margin-bottom:0pt">
<span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline">and it will give us a debian terminal where we can update and upgrade the system.</span></p>
<br><span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline"></span><p dir="ltr" style="line-height:1.15;margin-top:0pt;margin-bottom:0pt">
<span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline">To install mrtrix we need to use the neurodebian repository </span></p>
<h3 dir="ltr" style="line-height:1.15;margin-top:8pt;margin-bottom:0pt"><span style="font-size:15px;font-family:'Courier New';color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline">>wget -O- <a href="http://neuro.debian.net/lists/squeeze.de-m.full">http://neuro.debian.net/lists/squeeze.de-m.full</a> | sudo tee /etc/apt/sources.list.d/neurodebian.sources.list<br class="">
>sudo apt-key adv --recv-keys --keyserver <a href="http://pgp.mit.edu">pgp.mit.edu</a> 2649A5A9</span></h3><br><span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline"></span><p dir="ltr" style="line-height:1.15;margin-top:0pt;margin-bottom:0pt">
<span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline">If we use Lenny is necessary to change the neurodebian.sources.list and change squeeze for lenny.</span></p>
<br><span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline"></span><p dir="ltr" style="line-height:1.15;margin-top:0pt;margin-bottom:0pt">
<span style="font-size:15px;font-family:'Courier New';color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline">deb http:\\<a href="http://neurodebian.ovgu.de/debian">neurodebian.ovgu.de/debian</a> </span><span style="font-size:15px;font-family:'Courier New';color:rgb(0,0,0);background-color:transparent;font-weight:bold;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline">lenny</span><span style="font-size:15px;font-family:'Courier New';color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline"> main contrib non free</span><span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline"></span></p>
<br><span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline"></span><p dir="ltr" style="line-height:1.15;margin-top:0pt;margin-bottom:0pt">
<span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline">Now we can install mrtrix by typing:</span></p>
<br><span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline"></span><h3 dir="ltr" style="line-height:1.15;margin-top:8pt;margin-bottom:0pt">
<span style="font-size:15px;font-family:'Courier New';color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline">>sudo apt-get update</span></h3>
<h3 dir="ltr" style="line-height:1.15;margin-top:8pt;margin-bottom:0pt"><span style="font-size:15px;font-family:'Courier New';color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline">>sudo apt-get upgrade</span></h3>
<h3 dir="ltr" style="line-height:1.15;margin-top:8pt;margin-bottom:0pt"><span style="font-size:15px;font-family:'Courier New';color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline">>sudo apt-get install mrtrix</span></h3>
<br><span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline"></span><p dir="ltr" style="line-height:1.15;margin-top:0pt;margin-bottom:0pt">
<span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline">We can add the path for the binaries and libraries</span></p>
<h3 dir="ltr" style="line-height:1.15;margin-top:8pt;margin-bottom:0pt"><span style="font-size:15px;font-family:'Courier New';color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline">>export PATH=/usr/kerberos/sbin:/usr/kerberos/bin:/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/root/bin:/usr/lib/mrtrix/bin</span></h3>
<h3 dir="ltr" style="line-height:1.15;margin-top:8pt;margin-bottom:0pt"><span style="font-size:15px;font-family:'Courier New';color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline">> export LD_LIBRARY_PATH=/usr/lib/mrtrix/lib</span></h3>
<br><span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline"></span><p dir="ltr" style="line-height:1.15;margin-top:0pt;margin-bottom:0pt">
<span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline">At this point is easy to run the mrtrix binaries inside chroot, but it is possible to run them outside the chroot:</span></p>
<br><span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline"></span><h3 dir="ltr" style="line-height:1.15;margin-top:8pt;margin-bottom:0pt">
<span style="font-size:15px;font-family:'Courier New';color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline">schroot -p -c lenny/ /usr/lib/mrtrix/bin/streamtrack</span></h3>
<h3 dir="ltr" style="line-height:1.15;margin-top:8pt;margin-bottom:0pt"><span style="font-size:15px;font-family:'Courier New';color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline"> I: [lenny chroot] Running command:“/usr/lib/mrtrix/bin/streamtrack”</span></h3>
<h3 dir="ltr" style="line-height:1.15;margin-top:8pt;margin-bottom:0pt"><span style="font-size:15px;font-family:'Courier New';color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline"> streamtrack:expected exactly 3 arguments (0 supplied)</span></h3>
<br><span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline"></span><br><span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline"></span><span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline">So, here we are, issuing an mrtrix command from CentOS, but the actual command gets run by debian, transparently to the user. We have tested this even on a SunGridEngine cluster, and it works like a charm.</span><br>
<br><br id="docs-internal-guid-442b2180-30c2-1f4c-8211-1251620e3c02"><span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline"></span><p dir="ltr" style="line-height:1.15;margin-top:0pt;margin-bottom:0pt">
<span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:bold;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline">Note that if you are using a computing cluster, then schroot must be installed in every executing node</span><span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline">, and schroot.conf must point to the chroot, which must be accessible to the node.</span></p>
<br><span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline"></span><p dir="ltr" style="line-height:1.15;margin-top:0pt;margin-bottom:0pt">
<span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:bold;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline">For each executing node:</span></p>
<br><span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline"></span><p dir="ltr" style="line-height:1.15;margin-top:0pt;margin-bottom:0pt">
<span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline">Install boost libraries:</span></p>
<p dir="ltr" style="line-height:1.15;margin-top:0pt;margin-bottom:0pt"><span style="font-size:15px;font-family:'Courier New';color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline">yum install boost</span></p>
<br><span style="font-size:15px;font-family:'Courier New';color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline"></span><p dir="ltr" style="line-height:1.15;margin-top:0pt;margin-bottom:0pt">
<span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline">Update</span></p><p dir="ltr" style="line-height:1.15;margin-top:0pt;margin-bottom:0pt">
<span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline">bzip2-libs x86_64</span></p>
<br><span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline"></span><p dir="ltr" style="line-height:1.15;margin-top:0pt;margin-bottom:0pt">
<span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline">Also install the following dependencies:</span></p>
<p dir="ltr" style="line-height:1.15;margin-top:0pt;margin-bottom:0pt"><span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline">libicu</span></p>
<p dir="ltr" style="line-height:1.15;margin-top:0pt;margin-bottom:0pt"><span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline">bzip2-libs i386</span></p>
<br><span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline"></span><p dir="ltr" style="line-height:1.15;margin-top:0pt;margin-bottom:0pt">
<span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline">And accept the GPG key:</span></p>
<br><span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline"></span><p dir="ltr" style="line-height:1.15;margin-top:0pt;margin-bottom:0pt">
<a href="http://mirror.centos.org/centos/RPM-GPG-KEY-CentOS-5" style="text-decoration:none"><span style="font-size:15px;font-family:Arial;color:rgb(17,85,204);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:underline;vertical-align:baseline">http://mirror.centos.org/centos/RPM-GPG-KEY-CentOS-5</span></a></p>
<br><a href="http://mirror.centos.org/centos/RPM-GPG-KEY-CentOS-5" style="text-decoration:none"><span style="font-size:15px;font-family:Arial;color:rgb(17,85,204);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:underline;vertical-align:baseline"></span></a><p dir="ltr" style="line-height:1.15;margin-top:0pt;margin-bottom:0pt">
<span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline">Install lockdev</span></p>
<p dir="ltr" style="line-height:1.15;margin-top:0pt;margin-bottom:0pt"><span style="font-size:15px;font-family:'Courier New';color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline">yum install lockdev</span></p>
<br><span style="font-size:15px;font-family:'Courier New';color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline"></span><p dir="ltr" style="line-height:1.15;margin-top:0pt;margin-bottom:0pt">
<span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline">Install schroot</span></p>
<p dir="ltr" style="line-height:1.15;margin-top:0pt;margin-bottom:0pt"><span style="font-size:15px;font-family:'Courier New';color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline">rpm -Uvh schroot-1.1.5-4.x86_64.rpm</span></p>
<br><span style="font-size:15px;font-family:'Courier New';color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline"></span><span style="font-size:15px;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline">and, finally, edit etc/schroot/schroot.conf to point to the chroot, as described above. This node is ready to run debian!</span><br>
<br><br clear="all"><div><br></div>
</div></div></div></div>