Installation of SHOREmap v3.x
Prerequisites
Operating system
Currently, SHOREmap v3.x has been tested only on Linux Mint 14 Nadia with kernel 3.5.0-25-generic (x86_64. Check the bit-info of your operating system with 'uname -m'). The requirements on RAM and hard disk depend on the size of resequencing data. For Arabidopsis thaliana/Arabis alpina, it requires around 1GB RAM. Note that Linux Mint 14 Nadia is a bit old, you may try up to date systems like Linux Mint 18 (reports are welcomed if you have problems).
Download and Installation of library DISLIN
SHOREmap v3.x uses the scientific library DISLIN for data visualization. The Linux distribution of DISLIN requires the OpenMotif library libXm.so*, and libXt.so* (*note: for static compiling with dislin*.a, it may also require OpenGL library libGL.so as static compiling of openGL is always not suggested). If you do not have them installed on your operating system, please open a terminal application and install from the command line (note: this command requires root rights; if you do not have root rights, please ask the administrator for help)
Check if libXm.so* installed
ls /usr/lib/libXm.so*
If 'ls: cannot access /usr/lib/libXm.so*: No such file or directory' occurs, install it with
sudo apt-get update
sudo apt-get install libmotif4
Check again (and you should have them listed on the screen)
ls /usr/lib/libXm.so*
Check if libXt.so exists (note that 'x86_64' indicates your operating system is 64-bit; if you have a 32-bit operating system, you should replace 'x86_64' with 'i386' (i486, i586 etc) in all the following checking)
ls /usr/lib/x86_64-linux-gnu/libXt.so (or ls /usr/lib/i386-linux-gnu/libXt.so)
If 'ls: cannot access /usr/lib/x86_64-linux-gnu/libXt.so: No such file or directory' occurs, install it with
sudo apt-get install libxt-dev
(#answer 'y' if asked to continue!)
Then, check again,
ls /usr/lib/x86_64-linux-gnu/libXt.so (or ls /usr/lib/i386-linux-gnu/libXt.so)
Once the above is finished, download DISLIN to path/to/softwares/ (i.e., the folder where you want to store the installation-package-of-DISLIN) with the command (*note that the following assumes the system is 64-bit; if your system is 32-bit, please remove the suffix '_64' from the following commands)
wget ftp://ftp.gwdg.de/pub/grafik/dislin/linux/i586_64/dislin-11.0.linux.i586_64.deb -P path/to/softwares
Or,
wget ftp://ftp.gwdg.de/pub/grafik/dislin/linux/i586_64/dislin-11.0.linux.i586_64.tar.gz -P path/to/softwares
Correspondingly, there are two ways to install DISLIN. Installation with 'dislin-11.0.linux.i586_64.deb' is easier and thus recommended, by which there will be no further settings required for compiling SHOREmap. However, this requires that users have system-root right (sudo). If you have no such right, another way is to install DISLIN with 'dislin-11.0.linux.i586_64.tar.gz', for which several further settings have to be carried out for compiling SHOREmap properly. Specific commands for installing DISLIN in two ways are given below.
Installation of DISLIN with 'dislin-11.0.linux.i586_64.deb'. Change the working directory of the terminal to path/to/softwares with the command
cd path/to/softwares
Then execute the following command
sudo dpkg -i dislin-11.0.linux.i586_64.deb
By default, DISLIN is installed in /usr/local/dislin. Once the above is successfully finished, one can directly go to compile SHOREmap (in Section below: Download and Installation of SHOREmap v3.x).
Installation of DISLIN with 'dislin-11.0.linux.i586_64.tar.gz'. According to the manual of DISLIN,
1) Unpack the tar.gz file with the command
gzip -d dislin-11.0.linux.i586_64.tar.gz
2) Restore files from the tar file with the command
tar xvf dislin-11.0.linux.i586_64.tar
3) Change the working directory to the extraction directory of DISLIN with the command
cd dislin-11.0
Define an environment variable 'DISLIN' with a directory where DISLIN is expected to be installed. Supposing the directory is path/to/dislin/, type on the command line with
DISLIN=/path/to/dislin
export DISLIN
5) Run the install program with the command
./INSTALL
6) Copy dislin_d.h to folder dislin/
cp ./examples/dislin_d.h $DISLIN
(#answer 'y' if asked to overwrite!)
7) Delete directory 'dislin-11.0' (not necessarily) after installation with the commands
cd ..
rm -rf dislin-11.0
Download and Installation of SHOREmap v3.x
Opening a terminal, we can download SHOREmap v3.x (need to replace x with sub-version number, latest as v3.8) and store it in path/to/softwares with the command
mkdir softwares
wget http://bioinfo.mpipz.mpg.de/shoremap/SHOREmap_v3.x.tar.gz -P softwares
If you have downloaded SHOREmap_v3.x.tar.gz, then do the following
cd softwares
mkdir SHOREmap_v3.x
gzip -d SHOREmap_v3.x.tar.gz
tar xvf SHOREmap_v3.x.tar -C SHOREmap_v3.x
Get into SHOREmap_v3.x/ to compile SHOREmap. Remerber to carry out the following necessary settings for compiling if you have installed DISLIN with the tar.gz.
1) Replace some files in folder path/to/SHOREmap_v3.x/dislin
cd path/to/SHOREmap_v3.x/
rm dislin/*dislin_d.*
cp $DISLIN/*dislin_d.* dislin
(# $DISLIN is the path where you've installed dislin; answer 'y' if asked to overwrite!)
2) Open and edit /etc/profile (or .bashrc)
vi /etc/profile
Press key 'esc' and key 'i' to enter the edit mode of vi. If LD_LIBRARY_PATH already exists,insert the following statement into your /etc/profile,
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/path/to/SHOREmap_v3.x/dislin
Otherwise,
export LD_LIBRARY_PATH=/path/to/SHOREmap_v3.x/dislin
3) Save the changes and exit vi with :wq, and do the following
source /etc/profile
Exit the terminal and open a new one to make the above configure become active.
Now we enter path/to/softwares/SHOREmap_v3.x again with the command
cd path/to/softwares/SHOREmap_v3.x
Compilation of SHOREmap v3.x has been tested with g++ (Ubuntu/Linaro 4.7.2-2ubuntu1) 4.7.2 and g++ (Debian 4.7.2-5) 4.7.2 (earlier g++ versions might not work). Please check your g++ version with the command
g++ --version
if the screen information shows 'bash: g++: command not found', install it with
sudo apt-get install build-essential
#(answer 'y' if asked to continue!)
Suppose g++ is ready, compile the source codes with the command
make
Then a binary SHOREmap will be generated if the compilation is successfully finished.
Note 1: if the compilation complains like "/usr/bin/ld: cannot find -lXt" (or "/usr/bin/ld: cannot find -ldislin_d"), please open the makefile with the command
vi makefile
Press keys 'esc' and 'i' on the keyboard to edit makefile; move the cursor with arrow keys to the position before -lXt, and edit -L/path/to/libXt.so/; if '-ldislin_d' is not found, edit -L/path/to/dislin_d/ before -ldislin_d). After that, press keys 'esc', type in :wq, and press enter to save editing and quit vi. ('-L' tells the linker where to find the library given by -l)
Note 2: if '/usr/lib/ld: warning: libXm.so.3, needed by ./dislin/libdislin_d.so, not found (try using -rpath or -rpath-link)' occurs, and you have installed libmotif4, do the following:
cp /usr/lib/libXm.so.4 /usr/lib/libXm.so.3
We can make SHOREmap avaiable for general use by inserting the following command into /etc/profile
export PATH=$PATH:/path/to/SHOREmap_v3.x
and
source /etc/profile
To check what functions are incorporated in SHOREmap v3.x, we can type in the command below and press key 'enter'
SHOREmap
The following information will be printed on screen:
NOT enough input parameters. Check necessary parameters below:Usage of SHOREmap version 3.x: SHOREmap FUNCTION [OPTIONS]
FUNCTION is one of:
backcross analyzes backcrossing-derived mapping population
outcross analyzes outcrossing--derived mapping population
annotate annotates mutations based on gene feature (new: visualization of annotations is possible)
create creates markers according to two backgrounds
extract extracts base call info according to markers
convert converts VCF4.1 into acceptable formats; or (new) converts shore pileup into shore consensus_summary format
idFilter filters indels in one sample according to another (new)
about displays general/version/publication info about SHOREmap
For detailed COMMAND_arguments, please try: SHOREmap COMMAND
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