Ubuntu 22.04 Install instructions

Hi,

I have installed pharmit on my machine and thought I would share the install instructions so thay anyone with ubuntu 22.04 can run pharmit - as they are slightly different to the ubuntu 18 instuctions on the repo:

For reference my machine details are:

Distributor ID: Ubuntu
Description:    Ubuntu 22.04.4 LTS
Release:    22.04
Codename:   jammy

And to install pharm-it use the following instructions:

sudo apt install  git autoconf automake libtool ghostscript liblemon-dev libeigen3-dev libann-dev bmagic libcgicc-dev libgoogle-perftools-dev libglpk-dev coinor-* libjsoncpp-dev cmake libboost-dev swig libxml2-dev libcairo2-dev libboost-all-dev libcurl4-openssl-dev

git clone https://github.com/FastCGI-Archives/fcgi2.git
cd fcgi2
autoreconf -i
./configure
sudo make
sudo make install
cd ..

git clone https://github.com/openbabel/openbabel.git
cd openbabel
mkdir build
cd build
sudo cmake .. -DPYTHON_BINDINGS=1 -DRUN_SWIG=1  -DWITH_MAEPARSER=0 -DWITH_COORDGEN=0
sudo make -j12
sudo make install
cd ../..

git clone http://git.code.sf.net/p/smina/code smina
cd smina
mkdir build
cd build
sudo cmake ..
sudo make -j8
sudo cp libsmina.a /usr/local/lib/libsmina.a
cd ../..

git clone http://git.code.sf.net/p/pharmit/code pharmit
cd pharmit/src
mkdir build
cd build
#change `$path/smina` to the smina directory that reflects the install location from above
sudo cmake .. -DSMINALIB=/usr/local/lib/libsmina.a -DSMINA_DIR=$path/smina/ -DLEMON_DIR=/usr/lib/x86_64-linux-gnu/cmake/lemon/
sudo make -j12

Then run pharmit with ./pharmit --help and you should see this

./pharmit --help
USAGE: pharmit [options] --cmd command [pharma, dbcreate, dbcreateserverdir, dbsearch, server]

OPTIONS:
  -cmd=<string>         - command [pharma, dbcreate, dbcreateserverdir, dbsearch, server]
  -dbdir=<string>       - database directory(s)
  -dbinfo=<string>      - [dbcreateserverdir] JSON file describing database subset
  -extra-info           - Output additional molecular properties.  Slower.
  -file-partition       - Partion database slices based on files
  -help                 - Display available options (--help-hidden for more)
  -in=<string>          - input file(s)
  -ligs=<string>        - [dbcreateserverdir] Text file listing locations of molecules
  -logdir=<string>      - log directory for server
  -max-hits=<n>         - return at most n results
  -max-nrot=<uint>      - maximum allowed rotatable bonds
  -max-orient=<n>       - return at most n orientations of each conformation
  -max-rmsd=<number>    - maximum allowed RMSD; default max allowed by query
  -max-weight=<uint>    - maximum allowed molecular weight
  -min-nrot=<uint>      - minimum allowed rotatable bonds
  -min-port=<uint>      - port for minimization server
  -min-server=<string>  - minimization server address
  -min-weight=<uint>    - minimum allowed molecular weight
  -no-shape-index       - [dbcreateserverdir] Do not create shape indices
  -noindex              - [dbcreateserverdir] Do not create indices
  -nthreads=<n>         - utilize n threads; default 1
  -out=<string>         - output file(s)
  -pharmaspec=<string>  - pharmacophore specification
  -port=<uint>          - port for server to listen on
  -prefixes=<string>    - [dbcreateserverdir,server] File of directory prefixes to use for striping.
  -print                - print results
  -q                    - quiet; suppress informational messages
  -receptor=<string>    - Receptor file for interaction pharmacophroes
  -reduceconfs=<n>      - return at most n conformations for each molecule
  -show-query           - print query points
  -singledir=<string>   - Specify a single directory to recreate on a dbcreateserverdir command
  -singlesplit=<string> - Specify a single directory split to recreate on a dbcreateserverdir command
  -sort-rmsd            - Sort results by RMSD.
  -timestamp=<string>   - Specify timestamp to use for server dirs (for use with single)
  -unweighted-rmsd      - Compute minimal RMSD without radius weights

I hope this helps anyone trying to install on ubuntu 22.04

dkoes / pharmit

Ubuntu 22.04 Install instructions #1