Usage

PathwayMatcher can be used in different ways:

• Bioconda - using the Conda package manager
• Galaxy - using the Galaxy scientific workflow, data integration, data and analysis persistence and publishing platform
• Executable jar - using the java command line
• Docker container - using our Docker container

Bioconda

• Navigate to the folder where Bioconda installed PathwayMatcher.
• Execute the PathwayMatcher command.

The commands are the same as with the executable jar after replacing java -jar PathwayMatcher-X.Y.Z.jar with pathwaymatcher.

Example with a protein list:

pathwaymatcher match-uniprot [options]

Galaxy

PathwayMatcher is available as the reactome_pathwaymatcher Galaxy Tool in the Galaxy Tool Shed.

PathwayMatcher is already installed and ready to use into the official European Galaxy Instance.

In order to use reactome_pathwaymatcher in a Galaxy instance, you only need to:

• Choose the input type from the drop-down list.
• Upload a file (using the little button on the top left with an arrow pointing up) with data according to the input type chosen. It will be displayed on top of the history panel (on the right) in green when the upload finishes correctly.
• Click insert input if you want to add more inputs to PathwayMatcher.

When finish adding input files (and, if it is the case, output options), click Execute to run PathwayMatcher. Result files will be displayed in yellow in the history panel and (after a variable time depending on the complexity of the inputs) they will change to green when finish.

Executable JAR

• Navigate to the folder containing the PathwayMatcher .jar file. The file is name PathwayMatcher-X.Y.Z.jar, where X.Y.Z corresponds to the version number.
• Execute command on the .jar file.

Examples:

Protein list

java -jar PathwayMatcher-X.Y.Z.jar match-uniprot [options]

Example:

java -jar PathwayMatcher-X.Y.Z.jar match-ensembl -i <path/file_name> -o <path/file_name>

Proteoforms

List of proteins identified by Uniprot Accession number with associated post-translational modifications indicating the the MOD onthology ids and sites in the protein sequence.

java -jar PathwayMatcher-X.Y.Z.jar match-proteoforms -m <match_type> [options]

Peptide list

java -jar PathwayMatcher-X.Y.Z.jar match-peptides -f <path/fasta_file.fasta> [options]

Example:

java -jar PathwayMatcher-X.Y.Z.jar match-peptides -i <path/file_name> -f <path/fasta_file.fasta> -o <path/file_name>

Peptide list with PTMs

List of peptides with associated post-translational modifications indicating the the MOD onthology ids and sites in the protein sequence.

java -jar PathwayMatcher-X.Y.Z.jar match-modified-peptides -f <path/fasta_file.fasta> -m <match_type> [options]

SNPs

• List of rsId

java -jar PathwayMatcher-X.Y.Z.jar match-rsids -i ./snpList.txt -o ./output.csv [options]

• List of chromosome and base pairs

java -jar PathwayMatcher-X.Y.Z.jar match-chrbp -i ./variantList.txt -o ./output.csv [options]

Docker Container

In the Docker Terminal, run the command to start a new container myContainer from the PathwayMatcher image:

docker run \
    --v /<local_input_path>/:/<container_path/ \
    --v /<local_output_path>/:/<container_path>/ \
    --name myContainer \
    lfhs/pathwaymatcher:v1.9.1 <arguments>

• Note that <local_input_path> and <local_output_path> are absolute paths starting from "/".

The docker image is publicly available here. It gets downloaded at the moment of running in the Docker Terminal.

Example:

docker run \
    -v /c/Users/MyUser/input/:/home/input/ \
    -v /c/Users/MyUser/output/:/home/output/ \
 --name myContainer pathwaymatcher \
 match-uniprot \
 -i /home/input/inputFile.txt \
 -o /home/output/ \
 -T - g