Unable to locate quantisnp.exe in the GitHub repository

[lortsakahi]

Hi there,

I would like to use QuantiSNP to call CNVs from my genotyping SNP array but I cannot install it without the .exe file. Could you please update the repository so the file can be downloaded.

Best, Karin

[ConorBreen959]

I also have this issue.

The readme lists the following files to be used for installation:

    - Binary quantisnp (Linux) or quantisnp.exe (Windows).
    - Configuration files levels.dat and params.dat (levels-hd.dat is available for Infinium HD users).
    - Local GC content files for Build 35 and 36 of the human genome (b35.zip/b36.zip).
    - MATLAB Run-Time Libraries Installer (MCRInstallerXXX.bin - Linux, MCRInstallerXXX.exe - Windows).

I can only identify the configuration files in the repo.

[jtoloe]

Have a look at: https://github.com/hernanmd/QuantiSNP2

It provides the following snippet:

apt-get update
apt-get install bc wget mlocate unzip nano
cd /opt
wget ftp://ftp.stats.ox.ac.uk/pub/yau/quantisnp2/mcr/MCRinstaller64.run
chmod 755 MCRinstaller64.run
./MCRinstaller64.run  --noexec --keep --nox11 --target Install
cd Install
./MCRInstaller.bin -is:extract
cd istemp<tab>
chmod 755 jre1.5.0-linux-amd64.bin
./jre1.5.0-linux-amd64.bin
./bin/java -jar setup.jar -console
cd ../..
wget ftp://ftp.stats.ox.ac.uk/pub/yau/quantisnp2/executables/09042010/install_quantisnp
chmod 755 install_quantisnp
./install_quantisnp
wget ftp://ftp.stats.ox.ac.uk/pub/yau/quantisnp2/download/b37.tar.gz
cd quantisnp/examples

These instructions failed for me at the ./bin/java -jar setup.jar -console step, because the provided java version wouldn't run. I downloaded jdk-1_5_0_22-linux-amd64.bin from https://oracle.com and with that I was able to install the MCR. QuantiSNP now runs but I haven't tried it on any data yet.

[jtoloe]

I should add that these instructions are for the linux version of QuantiSNP2.