Docker wrapper around Bowtie genetic alignment search. All code is base to make it easier to run, as described in the project website Docker has to be installed on the computer before we can proceed. To do so, please refer to the Docker website for details on how to install it, and what version is needed for your computer.
Once Docker is successfully installed, download this repository
git clone https://github.com/ccivit/bowtie
cd bowtie
docker build -t bowtie .
docker run -v /user/dir/to/map:/bowtie -it bowtie
You need to download the files into the directory you determined above (/user/dir/to/map). This will be implemented as part of a setup.py file in the future.
wget https://sourceforge.net/projects/bowtie-bio/files/bowtie/1.3.0/bowtie-1.3.0-linux-x86_64.zip/download
unzip download
rm -r download
To test that the installation has gone correctly, you should be able to run without errors:
python bowtie e_coli reads/e_coli_1000.fq
As it is, t can only run wrappers found in the old FTP server. For example, if we want to run a sequence on s. cerevisiae. We first need to go into the index folder:
cd indexes
And download the indexes that we need:
wget ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/s_cerevisiae.ebwt.zip
unzip s_cerevisiae.ebwt.zip
Test if installation successful
cd ..
python bowtie -c s_cerevisiae ATTGTAGTTCGAGTAAGTAATGTGGGTTTG
output should be
Setting the index via positional argument will be deprecated in a future release. Please use -x option instead.
0 + Scchr02 90972 ATTGTAGTTCGAGTAAGTAATGTGGGTTTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIII 0
# reads processed: 1
# reads with at least one alignment: 1 (100.00%)
# reads that failed to align: 0 (0.00%)
Reported 1 alignments