From 4ee88475117233f48d5971aa50bd1c3fe113655a Mon Sep 17 00:00:00 2001 From: Cory Maughmer Date: Tue, 2 Jun 2020 17:47:26 -0500 Subject: [PATCH 1/5] Added testing information --- README.md | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) diff --git a/README.md b/README.md index 81b86ee3..184ddb73 100755 --- a/README.md +++ b/README.md @@ -18,6 +18,26 @@ The most commonly used tools have test cases built into the wrappper for code va Tools in this repository are designed for use inside of a Galaxy instance. Any use or installation independent of Galaxy, or outside the scope detailed for any given tool, is not supported. The CPT Galaxy instance hosts multiple tools produced by external groups which are not present in this repository. Some of these tools require additional permissions or licenses; please contact the relevant tool author(s) if you wish to host these on your Galaxy instance. +#### Deprecation Candidates + +Some tools are being set for deprecation and may be removed in future updates. + +Tool Name | Script Location | Reason +----------|-----------------|-------- +EFetch | edirect/efetch.xml | To be replaced with IUC version + +## Testing and Test Data +All tools present in the Structural, Functional, and Comparative workflows are testable with the `planemo test` command or via Galaxy's built in `run_tests.sh` script using the data in each subdirectory's `test-data` folder. The following tools are exceptions to this, as they rely on externally installed tools or services that are outside of Galaxy or Conda installed Packages. + +We are currently working to include these tests to all tools. + +Tool Name | Script Location +----------|----------------- +TMHMM (GFF3) | external/tmhmm.xml +[5.33-72.0] Interproscan functional predictions of ORFs | external/interproscan-5.33.xml +JBrowse 0.6.3+cpt | jbrowse/jbrowse.xml +progressiveMauve | comparative/progressivemauve.xml +All webapollo tools | webapollo/* ## Contribution From ffcd4e882c60c79692adfc39b6e12040f6efde22 Mon Sep 17 00:00:00 2001 From: Curtis Ross Date: Thu, 24 Sep 2020 14:36:40 -0500 Subject: [PATCH 2/5] update DOI --- README.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/README.md b/README.md index 184ddb73..e2129fa5 100755 --- a/README.md +++ b/README.md @@ -1,3 +1,5 @@ +![DOI](https://zenodo.org/badge/69267095.svg) + # CPT Galaxy Tools This is the collection of tools developed by the [Center for Phage Technology](https://cpt.tamu.edu/) for their Galaxy instance. The tool set is tailored for the analysis and annotation of bacteriophage genomes, but should also work well for prokaryotic genomes. From 7f235c51880744fc9aaa6eb4f7de58ab93b6597f Mon Sep 17 00:00:00 2001 From: Cory Maughmer Date: Mon, 26 Oct 2020 17:00:27 -0500 Subject: [PATCH 3/5] Update python, galaxy, planemo version --- .travis.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.travis.yml b/.travis.yml index 39c31f07..d48b4138 100644 --- a/.travis.yml +++ b/.travis.yml @@ -1,19 +1,19 @@ language: python -python: 2.7 +python: 3.7 git: submodules: false before_install: - export GALAXY_REPO=https://github.com/galaxyproject/galaxy - - export GALAXY_RELEASE=release_17.01 + - export GALAXY_RELEASE=release_20.05 - export PLANEMO_CONDA_PREFIX="$HOME/conda" - unset JAVA_HOME - git submodule init - git submodule update tools/one_snp_away install: - - pip install flake8 planemo==0.39 + - pip install flake8 planemo==0.62 - planemo conda_init - export PATH="$PLANEMO_CONDA_PREFIX/bin:$PATH" - conda create -y -q -c bioconda --name iuc_conda samtools=0.1.19 bcftools From f1789231549acc8d5b3050ba2c9de28407aea3fd Mon Sep 17 00:00:00 2001 From: Cory Maughmer Date: Tue, 27 Oct 2020 11:37:41 -0500 Subject: [PATCH 4/5] planemo version fix --- .travis.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index d48b4138..30236f7a 100644 --- a/.travis.yml +++ b/.travis.yml @@ -13,7 +13,7 @@ before_install: - git submodule update tools/one_snp_away install: - - pip install flake8 planemo==0.62 + - pip install flake8 planemo==0.72.0 - planemo conda_init - export PATH="$PLANEMO_CONDA_PREFIX/bin:$PATH" - conda create -y -q -c bioconda --name iuc_conda samtools=0.1.19 bcftools From e855bce171599e837953ae59de7c9102ca2a883f Mon Sep 17 00:00:00 2001 From: Cory Maughmer Date: Tue, 27 Oct 2020 13:18:58 -0500 Subject: [PATCH 5/5] Remove flake8 --- .travis.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index 30236f7a..a6267290 100644 --- a/.travis.yml +++ b/.travis.yml @@ -36,7 +36,7 @@ install: script: - set -e - - cd "$TRAVIS_BUILD_DIR" && flake8 --exclude=.git . + - cd "$TRAVIS_BUILD_DIR" - while read -r DIR; do planemo shed_lint --tools --ensure_metadata --urls --report_level warn --fail_level error --recursive "$DIR"; done < changed_repositories_chunk.list - while read -r DIR; do planemo conda_install "$DIR"; done < changed_repositories_chunk.list - while read -r DIR; do travis_wait 40 planemo test --conda_dependency_resolution --galaxy_branch "$GALAXY_RELEASE" --galaxy_source "$GALAXY_REPO" "$DIR"; done < changed_repositories_chunk.list