Install modeller with conda on Cent OS 7

It’s Friday after lunch here in Centreuropa so I’m going to be brief.  You may remember I previously built a Modeller 9.18 module on CentOS 7. Unfortunately it looks like the installation can’t be easily integrated with  CCP-EM. In this post, I will try an alternative installation method. Step 1 is to get Anaconda from the continuum repository:

wget http://repo.continuum.io/archive/Anaconda*-Linux-x86_64.sh

I will, as usual, show you the beginning and the end of the installation procedure, so you can cross-check it with your output. It starts here:

./Anaconda3-4.0.0-Linux-x86_64.sh
Welcome to Anaconda3 4.0.0 (by Continuum Analytics, Inc.)
In order to continue the installation process, 
please review the license
 agreement.
 Please, press ENTER to continue
 >>>
 ================
 Anaconda License
 ================

creating default environment...
 installation finished.
 Do you wish the installer to prepend the 
Anaconda3 install location
 to PATH in your /root/.bashrc ? [yes|no]
 [no] >>> yes
Prepending PATH=/usr/local/anaconda3/bin 
to PATH in /root/.bashrc
A backup will be made to: /root/.bashrc-anaconda3.bak
For this change to become active, 
you have to open a new terminal.
Thank you for installing Anaconda3!

And that was the end. Soft and sweet, as every professional product. Now we install modeller through it. It looks like the next:

> conda config --add channels salilab
> conda install modeller
 Using Anaconda Cloud api site https://api.anaconda.org
 Fetching package metadata: ......
 Solving package specifications: .........
Package plan for installation in environment 
/usr/local/anaconda3:

The following packages will be downloaded:

package              | build
---------------------|-----------------
 conda-env-2.6.0     | 0 502 B
 sqlite-3.13.0       | 0 4.0 MB
 xz-5.2.2            | 0 644 KB
 hdf5-1817-1.8.17    | 0 2.2 MB
 libtiff-4.0.6       | 2 1.5 MB
 python-3.5.3        | 1 15.9 MB
 anaconda-custom     | py35_0 3 KB
 modeller-9.18       | py35_1 17.5 MB
 requests-2.12.4     | py35_0 800 KB
 ruamel_yaml-0.11.14 | py35_1 395 KB
 cryptography-1.4    | py35_0 903 KB
 pyopenssl-16.2.0    | py35_0 70 KB
 conda-4.3.22        | py35_0 516 KB
 ---------------------------------
 Total: 44.3 MB

The following NEW packages will be INSTALLED:

hdf5-1817: 1.8.17-0
modeller: 9.18-py35_1
ruamel_yaml: 0.11.14-py35_1

The following packages will be UPDATED:

conda: 4.0.5-py35_0 --> 4.3.22-py35_0
conda-env: 2.4.5-py35_0 --> 2.6.0-0
cryptography: 1.3-py35_0 --> 1.4-py35_0
libtiff: 4.0.6-1 --> 4.0.6-2
pyopenssl: 0.15.1-py35_2 --> 16.2.0-py35_0
python: 3.5.1-0 --> 3.5.3-1
requests: 2.9.1-py35_0 --> 2.12.4-py35_0
sqlite: 3.9.2-0 --> 3.13.0-0
xz: 5.0.5-1 --> 5.2.2-0

The following packages will be DOWNGRADED:

anaconda: 4.0.0-np110py35_0 --> custom-py35_0

Proceed ([y]/n)? y

Fetching packages ...
 conda-env-2.6. 100% |#############| Time: 0:00:00 321.11 kB/s
...packages fetched! ...
 conda-4.3.22-p 100% |##########| Time: 0:00:00 26.19 MB/s
 Extracting packages ...
 [ COMPLETE ]|########################| 100%
 Unlinking packages ...
 [ COMPLETE ]|############################| 100%
 Linking packages ...
 [ COMPLETE ]|#############################| 100%

Edit /usr/local/
anaconda3/lib/modeller-9.18/modlib/modeller/config.py
and replace XXXX with your Modeller license key
(or set the KEY_MODELLER environment variable 
before running 'conda install').

On one side, it is nice that you have all the information. On the other side, now I have a custom conda installation, so if I need to install another package via conda, I will suffer. For ever. EVER. It’s either this or do a clean system install. Be warned!

Seriously, this is not easy. It’s like driving in the dark, blind folded, though a curvy road, in a country you don’t know, without driving license. You don’t know where you will end up. There you have it. Positive thinking to start with the weekend 😀

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About bitsanddragons

A traveller, an IT professional and a casual writer
This entry was posted in bits, centos, linux. Bookmark the permalink.

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