Results for "PA"
Bio-Scripts
Install Install Gffcompare on Ubuntu / Linux
#Gffcompare is a program that is used to perform...files. It has a binary distribution compatible with the linux we’re usi.... # download and extract cd ~/workspace/bin wget http://ccb.jhu.ed...e symlink ln -s ~/workspace/bin/gffcompare-0.9.8.Linux_x86_64/gffcompa...882 days ago
- ...s to their proper location and create symlinks for the executables. Finally we’d install the devtools and Biocmanager packages from the command line to make installing additional packages easier. We’ve commented...
882 days ago
Install StringTie on ubuntu / Linux !
...a symlink to make it easier to find. # download and extract cd ~/workspace/bin wget http://ccb.jhu.ed...-xzvf stringtie-1.3.0.Linux_x86_64.tar.gz # make symlink ln -s ~/workspace/bin/stringtie-1.3.0.Linux_x...882 days ago
Install Varscan on Ubuntu / Linux !
...rscan we simply need to download the distributed jar file into our ~/workspace/bin. As with the other java...tion we can invoke Varscan via java -jar. # Install Varscan cd ~/workspace/bin curl -L -k -o VarScan....882 days ago
- ...recommend running GATK through conda which is a package, environment, and depend...te, we can then run the program by providing the path to the executable. To exit...conda env create -f gatkcondaenv.yml -p ~/workspace/bin/conda/gatk # make sy...
870 days ago
Bash script to transfer files to server !
# rsync options source destination rsync -azvh --progress PacBio_clean.fa xxx@xxx.xxx.res.in:/home/ # scp source_file_name username@destination_host:destination_folder scp –rpv /datafile xxx@192.168.1.100:/home/me862 days ago
- ...- conda The following packages will be downloaded:...3.7 MB The following packages will be REMOVED: e...tils-xs-0.428-pl526_0 perl-pathtools-3.75-pl526h14c3975_1...################# | 100% Preparing transaction: done Verify...
844 days ago
- ...tgen-simulation-tools [sudo] password for neelam: Reading package lists... Done Building...it. The following additional packages will be installed: l..., 12.3 MB of additional disk space will be used. Do you want...lecting previously unselected package libgsl23:amd64. Prepari...
723 days ago
Conda command to install checkV
...- checkv The following packages will be downloaded:...25.9 MB The following NEW packages will be INSTALLED:...p-0.6.0-py_0 The following packages will be UPDATED: l...################# | 100% Preparing transaction: done Verify...694 days ago
Script to rapid genome clustering based on pairwise ANI
...pe nucl -out Next, use megablast from blast+ package to perform all-vs-all bl...entity 90 -o -num_threads 32 Next, calculate pairwise ANI by combining local...UST-like clustering using the MIUVIG recommended-parameters (95% ANI + 85% AF): a...694 days ago
