README_win_os.md

CoV-Seq: COVID-19 Genomic Sequence Database and Visualization

Notes for Windows OS:

Clone the repository

git clone https://github.com/boxiangliu/covseq.git

Git may automatically download and convert unix-format (EOL: \n) files in this repo into windows-format files (EOL: \r\n). To avoid it, the following command is needed before "git clone":

git config --global core.autocrlf false

Install Cygwin

Download Cygwin from here and add Cygwin (usually "C:\cygwin64\bin") into Windows Enviroment Variables PATH. And you may check its success by typing "bash" in a Windows CMD Prompt.

Install bcftools and htslib

Download both tools from here

First please install gcc (or g++) and the following dependencies from Cygwin:

BCFtools and HTSlib depend on the following libraries:

BCFtools:

zlib       <http://zlib.net> (---Cygwin package: zlib-devel 1.2.11-1)
gsl        <https://www.gnu.org/software/gsl/> (---Cygwin package: gsl 2.3-2)
           (optional, for the 'polysomy' command)
libperl    <http://www.perl.org/> (---Cygwin package: no need to install)
           (optional, to support filters using perl syntax)

HTSlib:

zlib       <http://zlib.net> (---Cygwin package: zlib-devel 1.2.11-1)
libbz2     <http://bzip.org/> (---Cygwin package: libbz2-devel 1.0.8-1) 
liblzma    <http://tukaani.org/xz/> (---Cygwin package: liblzma-devel 5.2.4-1)
libcurl    <https://curl.haxx.se/> (---Cygwin package: libcurl-devel 7.66.0-1)
           (optional but strongly recommended, for network access)
libcrypto  <https://www.openssl.org/> (---Cygwin package: no need to install)
           (optional, for Amazon S3 support; not needed on MacOS)

Please refer to the file INSTALL in bcftools.x and htslib.x for more details.

Then add the bcftools and htslib bin path into Windows Enviroment Variables PATH.

Install Java:

Download jdk-14.0.1_windows-x64_bin.zip from here and add into PATH.

Install MAFFT:

Install MAFFT and add into PATH.