This guide is for updating your SeqWare Command Line Executable (CLI) executable to work with new (or old) versions of SeqWare.
Download the version of SeqWare that you need from Artifactory. Make sure you copy the one JAR with “-full” at the end of its name, e.g. seqware-distribution-1.1.0.jar
user@localhost:~$ wget https://seqwaremaven.oicr.on.ca/artifactory/simple/seqware-release/com/github/seqware/seqware-distribution/1.1.0/seqware-distribution-1.1.0-full.jar
Copy this jar to your seqware self-installs directory.
user@localhost:~$ mv seqware-distribution-1.1.0-full.jar ~/.seqware/self-installs
Open up your ~/bin/seqware script that you had installed previously and change the SeqWare version to the newest one by editing “DEFAULT_SEQWARE_VERSION”. Make sure that the name exactly matches what the JAR is called.
#!/usr/bin/env bash # Ensure this file is executable via `chmod a+x seqware`, then place it # somewhere on your $PATH, like ~/bin. The rest of SeqWare will be # installed upon first run into the ~/.seqware directory. DEFAULT_SEQWARE_VERSION="1.1.0"
seqware with no arguments. This will trigger SeqWare to download the sanity check file that corresponds to the new version.
someUser@someHost:~$ seqware Downloading SeqWare Check to /home/someUser/.seqware/self-installs/seqware-sanity-check-1.1.0-jar-paired-with-distribution.jar now... % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 174k 100 174k 0 0 7158k 0 --:--:-- --:--:-- --:--:-- 7262k Usage: seqware [<flag>] seqware <command> [--help] Commands: annotate Add arbitrary key/value pairs to seqware objects query Display ad-hoc information about seqware objects bundle Interact with a workflow bundle during development/admin copy Copy files between local and remote file systems create Create new seqware objects (e.g., study) files Extract information about workflow output files study Extract information about studies workflow Interact with workflows workflow-run Interact with workflow runs checkdb Check the seqware database for convention errors check Check the seqware environment for configuration issues dev Advanced commands that are useful for developers or debugging Flags: --help Print help out --version Print Seqware's version --metadata Print metadata environment