### Install Miniconda3 Source: https://github.com/xiezhq/isescan/blob/master/README.md Executes the installer script to set up the Miniconda environment. ```bash sh Miniconda3-latest-Linux-x86_64.sh ``` -------------------------------- ### Download Miniconda3 Installer Source: https://github.com/xiezhq/isescan/blob/master/README.md Downloads the latest Miniconda3 Linux installer script. ```bash curl -O https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh ``` -------------------------------- ### Initialize Miniconda3 Source: https://github.com/xiezhq/isescan/blob/master/README.md Enables conda initialization during the installation process. ```text Do you wish the installer to initialize Miniconda3 by running conda init? [yes|no] [no] >>> yes ``` -------------------------------- ### Manually Install ISEScan Source Source: https://github.com/xiezhq/isescan/blob/master/README.md Extracts the source archive and overwrites existing Python files in the installation directory. ```bash tar -zxf v1.7.2.2.2.tar.gz cd ISEScan-1.7.2.2.2/ cp *.py /apps/inst/miniconda3/bin/ ``` -------------------------------- ### Cleanup and Source Configuration Source: https://github.com/xiezhq/isescan/blob/master/README.md Removes the installer script and refreshes the shell environment. ```bash rm Miniconda3-latest-Linux-x86_64.sh source ~/.bashrc ``` -------------------------------- ### Install ISEScan via Conda Source: https://github.com/xiezhq/isescan/blob/master/README.md Installs the ISEScan package from the bioconda channel. ```bash conda install isescan ``` -------------------------------- ### Example genome list file format Source: https://github.com/xiezhq/isescan/blob/master/README.md The expected format for the input list file containing paths to FASTA files. ```text /N/dc2/scratch/zhiqxie/hmp/HMASM/SRS014235.scaffolds.fa /N/dc2/scratch/zhiqxie/hmp/HMASM/SRS049959.scaffolds.fa /N/dc2/scratch/zhiqxie/hmp/HMASM/SRS020233.scaffolds.fa /N/dc2/scratch/zhiqxie/hmp/HMASM/SRS022609.scaffolds.fa /N/dc2/scratch/zhiqxie/hmp/HMASM/SRS024132.scaffolds.fa ``` -------------------------------- ### Run ISEScan on a single genome Source: https://github.com/xiezhq/isescan/blob/master/README.md Basic commands to execute ISEScan depending on the installation method. ```bash conda activate base isescan.py --seqfile NC_012624.fna --output results ``` ```bash python3 /home/xiezhq/projects/ISEScan-1.7.2.2/isescan.py --seqfile genome1.fa --output results ``` -------------------------------- ### Verify ISEScan Version Source: https://github.com/xiezhq/isescan/blob/master/README.md Checks the currently installed version of ISEScan. ```bash python3 isescan.py --version ``` ```bash isescan.py --version ``` -------------------------------- ### Test ISEScan Execution Source: https://github.com/xiezhq/isescan/blob/master/README.md Runs a test analysis on a sequence file to confirm the installation is working correctly. ```bash python3 isescan.py --seqfile /apps/inst/miniconda3/test/NC_012624.fna --output /home/xiezhq/results --nthread 2 ``` -------------------------------- ### Locate ISEScan Installation Source: https://github.com/xiezhq/isescan/blob/master/README.md Identifies the directory where the ISEScan executable is located. ```bash which isescan.py /apps/inst/miniconda3/bin/isescan.py ``` -------------------------------- ### Configure SSW library path Source: https://github.com/xiezhq/isescan/blob/master/README.md Copy the compiled library and update the library search path. ```bash cp libssw.so ../ export LD_LIBRARY_PATH=/home/xiezhq/projects/ISEScan-1.7.2.2:$LD_LIBRARY_PATH ``` -------------------------------- ### Compile SSW library Source: https://github.com/xiezhq/isescan/blob/master/README.md Compile the bundled SSW library using gcc. ```bash cd ssw201507 gcc -Wall -O3 -pipe -fPIC -shared -rdynamic -o libssw.so ssw.c ssw.h ``` -------------------------------- ### Update system PATH for dependencies Source: https://github.com/xiezhq/isescan/blob/master/README.md Add the directories containing required bioinformatics tools to the system PATH. ```bash export PATH=$PATH:/apps/inst/FragGeneScan1.30:/apps/inst/hmmer-3.3/bin:/apps/inst/ncbi-blast-2.10.0+/bin ``` -------------------------------- ### Configure Conda Channels Source: https://github.com/xiezhq/isescan/blob/master/README.md Adds necessary channels to conda with correct priority settings. ```bash conda config --add channels defaults conda config --add channels bioconda conda config --add channels conda-forge ``` -------------------------------- ### Navigate to ISEScan directory Source: https://github.com/xiezhq/isescan/blob/master/README.md Change directory to the extracted ISEScan folder. ```bash cd ISEScan-1.7.2.2 ``` -------------------------------- ### Update System PATH Source: https://github.com/xiezhq/isescan/blob/master/README.md Adds the ISEScan binary directory to the system PATH if the command is not found. ```bash export PATH=/apps/inst/miniconda3/bin/:$PATH ``` -------------------------------- ### Uncompress ISEScan source files Source: https://github.com/xiezhq/isescan/blob/master/README.md Commands to extract the downloaded source archive. ```bash unzip v1.7.2.2.zip ``` ```bash tar -zvxf v1.7.2.2.tar.gz ``` -------------------------------- ### Run ISEScan Analysis Source: https://github.com/xiezhq/isescan/blob/master/README.md Executes ISEScan on a sequence file with specified output directory and thread count. ```bash cp /apps/inst/miniconda3/test/NC_012624.fna ./ isescan.py --seqfile NC_012624.fna --output results --nthread 2 ``` -------------------------------- ### Configure ISEScan thread usage Source: https://github.com/xiezhq/isescan/blob/master/README.md Adjust the number of CPU cores used by ISEScan during execution. ```bash isescan.py --seqfile genome1.fa --output results --nthread 2 ``` -------------------------------- ### Upgrade ISEScan via Bioconda Source: https://github.com/xiezhq/isescan/blob/master/README.md Updates an existing Bioconda-installed ISEScan instance to the latest available version. ```bash conda update isescan ``` -------------------------------- ### Execute ISEScan in parallel for multiple genomes Source: https://github.com/xiezhq/isescan/blob/master/README.md Run multiple ISEScan jobs concurrently using xargs to process a list of genome files. ```bash nohup cat test.fna.list | xargs -n 1 -P 4 -I{} isescan.py --seqfile {} --output results --nthread 2 > log.txt & ``` -------------------------------- ### Retry ISEScan Analysis Source: https://github.com/xiezhq/isescan/blob/master/README.md Executes the analysis command after updating the PATH. ```bash isescan.py --seqfile NC_012624.fna --output results --nthread 2 ``` -------------------------------- ### Re-run ISEScan Source: https://github.com/xiezhq/isescan/blob/master/README.md Command to re-run ISEScan after removing intermediate files to force recalculation. ```bash isescan.py --seqfile NC_012624.fna --output results ``` === COMPLETE CONTENT === This response contains all available snippets from this library. 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