201027 catchup

.travis.yml

@@ -13,7 +13,7 @@ before_install:
   - git submodule update tools/one_snp_away
 
 install:
-  - pip install flake8 planemo==0.62
+  - pip install 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
@@ -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

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. 
@@ -39,7 +41,6 @@ JBrowse 0.6.3+cpt | jbrowse/jbrowse.xml
 progressiveMauve | comparative/progressivemauve.xml
 All webapollo tools | webapollo/*
 
-
 ## Contribution
 
 When contributing new tools or bugfixes to this repo, ensure that you apply [Black code formatting](https://github.com/psf/black) first.