### applied-bioinformatics
[src/applied-bioinformatics/An-Introduction-To-Applied-Bioinformatics]
checkout = git clone https://github.com/applied-bioinformatics/An-Introduction-To-Applied-Bioinformatics An-Introduction-To-Applied-Bioinformatics && \
    cd An-Introduction-To-Applied-Bioinformatics && \
    git remote rename origin applied-bioinformatics && \
    git remote add thermokarst https://github.com/thermokarst/An-Introduction-To-Applied-Bioinformatics && \
    git fetch thermokarst


### biocore
checkout = git clone https://github.com/biocore/deblur deblur && \
    cd deblur && \
    git remote rename origin biocore && \
    git remote add thermokarst https://github.com/thermokarst/deblur && \
    git fetch thermokarst

checkout = git clone https://github.com/biocore/scikit-bio scikit-bio && \
    cd scikit-bio && \
    git remote rename origin biocore && \
    git remote add ElDeveloper https://github.com/ElDeveloper/scikit-bio && \
    git remote add ebolyen https://github.com/ebolyen/scikit-bio && \
    git remote add wasade https://github.com/wasade/scikit-bio && \
    git remote add thermokarst https://github.com/thermokarst/scikit-bio && \
    git fetch thermokarst


### caporaso-lab
[src/caporaso-lab/SurveySync]
checkout = git clone https://github.com/caporaso-lab/SurveySync SurveySync && \
    cd SurveySync && \
    git remote rename origin caporaso-lab && \
    git remote add turanoo https://github.com/turanoo/SurveySync && \
    git remote add thermokarst https://github.com/thermokarst/SurveySync && \
    git fetch thermokarst

[src/caporaso-lab/caporaso-lab.github.io]
checkout = git clone https://github.com/caporaso-lab/caporaso-lab.github.io caporaso-lab.github.io && \
    cd caporaso-lab.github.io && \
    git remote rename origin caporaso-lab && \
    git remote add thermokarst https://github.com/thermokarst/caporaso-lab.github.io && \
    git fetch thermokarst

[src/caporaso-lab/sc18-poster]
checkout = git clone https://github.com/caporaso-lab/sc18-poster sc18-poster && \
    cd sc18-poster && \
    git remote rename origin caporaso-lab && \
    git remote add thermokarst https://github.com/thermokarst/sc18-poster && \
    git fetch thermokarst

[src/caporaso-lab/pretrained-feature-classifiers]
checkout = git clone https://github.com/caporaso-lab/pretrained-feature-classifiers pretrained-feature-classifiers && \
    cd pretrained-feature-classifiers && \
    git remote rename origin caporaso-lab && \
    git remote add thermokarst https://github.com/thermokarst/pretrained-feature-classifiers && \
    git fetch thermokarst


### qiime2
[src/qiime2/Keemei]
checkout = git clone https://github.com/qiime2/Keemei Keemei && \
    cd Keemei && \
    git remote rename origin qiime2 && \
    git remote add thermokarst https://github.com/thermokarst/Keemei && \
    git fetch thermokarst

[src/qiime2/busywork]
checkout = git clone https://github.com/qiime2/busywork busywork && \
    cd busywork && \
    git remote rename origin qiime2 && \
    git remote add thermokarst https://github.com/thermokarst/busywork && \
    git fetch thermokarst

[src/qiime2/data.qiime2.org]
checkout = git clone https://github.com/qiime2/data.qiime2.org data.qiime2.org && \
    cd data.qiime2.org && \
    git remote rename origin qiime2 && \
    git remote add thermokarst https://github.com/thermokarst/data.qiime2.org && \
    git fetch thermokarst

[src/qiime2/dev-docs]
checkout = git clone https://github.com/qiime2/dev-docs dev-docs && \
    cd dev-docs && \
    git remote rename origin qiime2 && \
    git remote add thermokarst https://github.com/thermokarst/dev-docs && \
    git fetch thermokarst

[src/qiime2/discourse-unhandled-tagger]
checkout = git clone https://github.com/qiime2/discourse-unhandled-tagger discourse-unhandled-tagger && \
    cd discourse-unhandled-tagger && \
    git remote rename origin qiime2 && \
    git remote add thermokarst https://github.com/thermokarst/discourse-unhandled-tagger && \
    git fetch thermokarst

[src/qiime2/docs]
checkout = git clone https://github.com/qiime2/docs docs && \
    cd docs && \
    git remote rename origin qiime2 && \
    git remote add ChrisKeefe https://github.com/ChrisKeefe/docs && \
    git remote add antgonza https://github.com/antgonza/docs && \
    git remote add cduvallet https://github.com/cduvallet/docs && \
    git remote add ebolyen https://github.com/ebolyen/docs && \
    git remote add nbokulich https://github.com/nbokulich/docs && \
    git remote add turanoo https://github.com/turanoo/docs && \
    git remote add gregcaporaso https://github.com/gregcaporaso/docs && \
    git remote add thermokarst https://github.com/thermokarst/docs && \
    git fetch thermokarst

[src/qiime2/environment-files]
checkout = git clone https://github.com/qiime2/environment-files environment-files && \
    cd environment-files && \
    git remote rename origin qiime2 && \
    git remote add thermokarst https://github.com/thermokarst/environment-files && \
    git fetch thermokarst

[src/qiime2/library]
checkout = git clone https://github.com/qiime2/library library && \
    cd library && \
    git remote rename origin qiime2 && \
    git remote add thermokarst https://github.com/thermokarst/library && \
    git fetch thermokarst

[src/qiime2/logos]
checkout = git clone https://github.com/qiime2/logos logos && \
    cd logos && \
    git remote rename origin qiime2 && \
    git remote add thermokarst https://github.com/thermokarst/logos && \
    git fetch thermokarst

[src/qiime2/q2-alignment]
checkout = git clone https://github.com/qiime2/q2-alignment q2-alignment && \
    cd q2-alignment && \
    git remote rename origin qiime2 && \
    git remote add turanoo https://github.com/turanoo/q2-alignment && \
    git remote add thermokarst https://github.com/thermokarst/q2-alignment && \
    git fetch thermokarst

[src/qiime2/q2-composition]
checkout = git clone https://github.com/qiime2/q2-composition q2-composition && \
    cd q2-composition && \
    git remote rename origin qiime2 && \
    git remote add nbokulich https://github.com/nbokulich/q2-composition && \
    git remote add thermokarst https://github.com/thermokarst/q2-composition && \
    git fetch thermokarst

[src/qiime2/q2-cutadapt]
checkout = git clone https://github.com/qiime2/q2-cutadapt q2-cutadapt && \
    cd q2-cutadapt && \
    git remote rename origin qiime2 && \
    git remote add ebolyen https://github.com/ebolyen/q2-cutadapt && \
    git remote add thermokarst https://github.com/thermokarst/q2-cutadapt && \
    git fetch thermokarst

[src/qiime2/q2-dada2]
checkout = git clone https://github.com/qiime2/q2-dada2 q2-dada2 && \
    cd q2-dada2 && \
    git remote rename origin qiime2 && \
    git remote add benjjneb https://github.com/benjjneb/q2-dada2 && \
    git remote add ebolyen https://github.com/ebolyen/q2-dada2 && \
    git remote add thermokarst https://github.com/thermokarst/q2-dada2 && \
    git fetch thermokarst

[src/qiime2/q2-deblur]
checkout = git clone https://github.com/qiime2/q2-deblur q2-deblur && \
    cd q2-deblur && \
    git remote rename origin qiime2 && \
    git remote add thermokarst https://github.com/thermokarst/q2-deblur && \
    git fetch thermokarst

[src/qiime2/q2-demux]
checkout = git clone https://github.com/qiime2/q2-demux q2-demux && \
    cd q2-demux && \
    git remote rename origin qiime2 && \
    git remote add thermokarst https://github.com/thermokarst/q2-demux && \
    git fetch thermokarst

[src/qiime2/q2-diversity]
checkout = git clone https://github.com/qiime2/q2-diversity q2-diversity && \
    cd q2-diversity && \
    git remote rename origin qiime2 && \
    git remote add ChrisKeefe https://github.com/ChrisKeefe/q2-diversity && \
    git remote add ElDeveloper https://github.com/ElDeveloper/q2-diversity && \
    git remote add ebolyen https://github.com/ebolyen/q2-diversity && \
    git remote add nbokulich https://github.com/nbokulich/q2-diversity && \
    git remote add thermokarst https://github.com/thermokarst/q2-diversity && \
    git fetch thermokarst

[src/qiime2/q2-diversity-lib]
checkout = git clone https://github.com/qiime2/q2-diversity-lib q2-diversity-lib && \
    cd q2-diversity-lib && \
    git remote rename origin qiime2 && \
    git remote add ChrisKeefe https://github.com/ChrisKeefe/q2-diversity-lib && \
    git remote add thermokarst https://github.com/thermokarst/q2-diversity-lib && \
    git fetch thermokarst

[src/qiime2/q2-emperor]
checkout = git clone https://github.com/qiime2/q2-emperor q2-emperor && \
    cd q2-emperor && \
    git remote rename origin qiime2 && \
    git remote add ElDeveloper https://github.com/ElDeveloper/q2-emperor && \
    git remote add thermokarst https://github.com/thermokarst/q2-emperor && \
    git fetch thermokarst

[src/qiime2/q2-feature-classifier]
checkout = git clone https://github.com/qiime2/q2-feature-classifier q2-feature-classifier && \
    cd q2-feature-classifier && \
    git remote rename origin qiime2 && \
    git remote add nbokulich https://github.com/nbokulich/q2-feature-classifier && \
    git remote add thermokarst https://github.com/thermokarst/q2-feature-classifier && \
    git fetch thermokarst

[src/qiime2/q2-feature-table]
checkout = git clone https://github.com/qiime2/q2-feature-table q2-feature-table && \
    cd q2-feature-table && \
    git remote rename origin qiime2 && \
    git remote add ebolyen https://github.com/ebolyen/q2-feature-table && \
    git remote add gregcaporaso https://github.com/gregcaporaso/q2-feature-table && \
    git remote add wasade https://github.com/wasade/q2-feature-table && \
    git remote add thermokarst https://github.com/thermokarst/q2-feature-table && \
    git fetch thermokarst

[src/qiime2/q2-fragment-insertion]
checkout = git clone https://github.com/qiime2/q2-fragment-insertion q2-fragment-insertion && \
    cd q2-fragment-insertion && \
    git remote rename origin qiime2 && \
    git remote add thermokarst https://github.com/thermokarst/q2-fragment-insertion && \
    git fetch thermokarst

[src/qiime2/q2-gneiss]
checkout = git clone https://github.com/qiime2/q2-gneiss q2-gneiss && \
    cd q2-gneiss && \
    git remote rename origin qiime2 && \
    git remote add thermokarst https://github.com/thermokarst/q2-gneiss && \
    git fetch thermokarst

[src/qiime2/q2-longitudinal]
checkout = git clone https://github.com/qiime2/q2-longitudinal q2-longitudinal && \
    cd q2-longitudinal && \
    git remote rename origin qiime2 && \
    git remote add nbokulich https://github.com/nbokulich/q2-longitudinal && \
    git remote add thermokarst https://github.com/thermokarst/q2-longitudinal && \
    git fetch thermokarst

[src/qiime2/q2-metadata]
checkout = git clone https://github.com/qiime2/q2-metadata q2-metadata && \
    cd q2-metadata && \
    git remote rename origin qiime2 && \
    git remote add thermokarst https://github.com/thermokarst/q2-metadata && \
    git fetch thermokarst

[src/qiime2/q2-phylogeny]
checkout = git clone https://github.com/qiime2/q2-phylogeny q2-phylogeny && \
    cd q2-phylogeny && \
    git remote rename origin qiime2 && \
    git remote add mikerobeson https://github.com/mikerobeson/q2-phylogeny && \
    git remote add thermokarst https://github.com/thermokarst/q2-phylogeny && \
    git fetch thermokarst

[src/qiime2/q2-quality-control]
checkout = git clone https://github.com/qiime2/q2-quality-control q2-quality-control && \
    cd q2-quality-control && \
    git remote rename origin qiime2 && \
    git remote add nbokulich https://github.com/nbokulich/q2-quality-control && \
    git remote add thermokarst https://github.com/thermokarst/q2-quality-control && \
    git fetch thermokarst

[src/qiime2/q2-quality-filter]
checkout = git clone https://github.com/qiime2/q2-quality-filter q2-quality-filter && \
    cd q2-quality-filter && \
    git remote rename origin qiime2 && \
    git remote add thermokarst https://github.com/thermokarst/q2-quality-filter && \
    git fetch thermokarst

[src/qiime2/q2-sample-classifier]
checkout = git clone https://github.com/qiime2/q2-sample-classifier q2-sample-classifier && \
    cd q2-sample-classifier && \
    git remote rename origin qiime2 && \
    git remote add BenKaehler https://github.com/BenKaehler/q2-sample-classifier && \
    git remote add nbokulich https://github.com/nbokulich/q2-sample-classifier && \
    git remote add thermokarst https://github.com/thermokarst/q2-sample-classifier && \
    git fetch thermokarst

[src/qiime2/q2-taxa]
checkout = git clone https://github.com/qiime2/q2-taxa q2-taxa && \
    cd q2-taxa && \
    git remote rename origin qiime2 && \
    git remote add thermokarst https://github.com/thermokarst/q2-taxa && \
    git fetch thermokarst

[src/qiime2/q2-types]
checkout = git clone https://github.com/qiime2/q2-types q2-types && \
    cd q2-types && \
    git remote rename origin qiime2 && \
    git remote add thermokarst https://github.com/thermokarst/q2-types && \
    git fetch thermokarst

[src/qiime2/q2-vsearch]
checkout = git clone https://github.com/qiime2/q2-vsearch q2-vsearch && \
    cd q2-vsearch && \
    git remote rename origin qiime2 && \
    git remote add thermokarst https://github.com/thermokarst/q2-vsearch && \
    git fetch thermokarst

[src/qiime2/q2cli]
checkout = git clone https://github.com/qiime2/q2cli q2cli && \
    cd q2cli && \
    git remote rename origin qiime2 && \
    git remote add ebolyen https://github.com/ebolyen/q2cli && \
    git remote add turanoo https://github.com/turanoo/q2cli && \
    git remote add thermokarst https://github.com/thermokarst/q2cli && \
    git fetch thermokarst

[src/qiime2/q2cwl]
checkout = git clone https://github.com/qiime2/q2cwl q2cwl && \
    cd q2cwl && \
    git remote rename origin qiime2 && \
    git remote add ebolyen https://github.com/ebolyen/q2cwl && \
    git remote add thermokarst https://github.com/thermokarst/q2cwl && \
    git fetch thermokarst

[src/qiime2/q2galaxy]
checkout = git clone https://github.com/qiime2/q2galaxy q2galaxy && \
    cd q2galaxy && \
    git remote rename origin qiime2 && \
    git remote add ebolyen https://github.com/ebolyen/q2galaxy && \
    git remote add thermokarst https://github.com/thermokarst/q2galaxy && \
    git fetch thermokarst

[src/qiime2/galaxy]
checkout = git clone https://github.com/galaxyproject/galaxy galaxy && \
    cd galaxy && \
    git remote rename origin galaxyproject && \
    git remote add ebolyen https://github.com/ebolyen/galaxy && \
    git remote add thermokarst https://github.com/thermokarst/galaxy && \
    git fetch thermokarst

[src/qiime2/q2studio]
checkout = git clone https://github.com/qiime2/q2studio q2studio && \
    cd q2studio && \
    git remote rename origin qiime2 && \
    git remote add thermokarst https://github.com/thermokarst/q2studio && \
    git fetch thermokarst

[src/qiime2/q2templates]
checkout = git clone https://github.com/qiime2/q2templates q2templates && \
    cd q2templates && \
    git remote rename origin qiime2 && \
    git remote add thermokarst https://github.com/thermokarst/q2templates && \
    git fetch thermokarst

[src/qiime2/q2view]
checkout = git clone https://github.com/qiime2/q2view q2view && \
    cd q2view && \
    git remote rename origin qiime2 && \
    git remote add ebolyen https://github.com/ebolyen/q2view && \
    git remote add turanoo https://github.com/turanoo/q2view && \
    git remote add thermokarst https://github.com/thermokarst/q2view && \
    git fetch thermokarst

[src/qiime2/qiime2]
checkout = git clone https://github.com/qiime2/qiime2 qiime2 && \
    cd qiime2 && \
    git remote rename origin qiime2 && \
    git remote add ebolyen https://github.com/ebolyen/qiime2 && \
    git remote add thermokarst https://github.com/thermokarst/qiime2 && \
    git fetch thermokarst

[src/qiime2/qiime2.github.io]
checkout = git clone https://github.com/qiime2/qiime2.github.io qiime2.github.io && \
    cd qiime2.github.io && \
    git remote rename origin qiime2 && \
    git remote add thermokarst https://github.com/thermokarst/qiime2.github.io && \
    git fetch thermokarst

[src/qiime2/template-repo]
checkout = git clone https://github.com/qiime2/template-repo template-repo && \
    cd template-repo && \
    git remote rename origin qiime2 && \
    git remote add thermokarst https://github.com/thermokarst/template-repo && \
    git fetch thermokarst

[src/qiime2/view.qiime2.org]
checkout = git clone https://github.com/qiime2/view.qiime2.org view.qiime2.org && \
    cd view.qiime2.org && \
    git remote rename origin qiime2 && \
    git remote add thermokarst https://github.com/thermokarst/view.qiime2.org && \
    git fetch thermokarst

[src/qiime2/vm-playbooks]
checkout = git clone https://github.com/qiime2/vm-playbooks vm-playbooks && \
    cd vm-playbooks && \
    git remote rename origin qiime2 && \
    git remote add thermokarst https://github.com/thermokarst/vm-playbooks && \
    git fetch thermokarst

[src/qiime2/workshop-playbooks]
checkout = git clone https://github.com/qiime2/workshop-playbooks workshop-playbooks && \
    cd workshop-playbooks && \
    git remote rename origin qiime2 && \
    git remote add thermokarst https://github.com/thermokarst/workshop-playbooks && \
    git fetch thermokarst

[src/qiime2/workshops.qiime2.org]
checkout = git clone https://github.com/qiime2/workshops.qiime2.org workshops.qiime2.org && \
    cd workshops.qiime2.org && \
    git remote rename origin qiime2 && \
    git remote add thermokarst https://github.com/thermokarst/workshops.qiime2.org && \
    git fetch thermokarst


### gregcaporaso
[src/gregcaporaso/caporaso-lab-secrets]
checkout = git clone https://github.com/gregcaporaso/caporaso-lab-secrets && \
    cd caporaso-lab-secrets && \
    git remote rename origin gregcaporaso && \
    git remote add thermokarst https://github.com/thermokarst/caporaso-lab-secrets && \
    git fetch thermokarst

[src/gregcaporaso/qiime2-meta-figures]
checkout = git clone https://github.com/gregcaporaso/qiime2-meta-figures && \
    cd qiime2-meta-figures && \
    git remote rename origin gregcaporaso && \
    git remote add thermokarst https://github.com/thermokarst/qiime2-meta-figures && \
    git fetch thermokarst

[src/gregcaporaso/workshop-tutorials]
checkout = git clone https://github.com/gregcaporaso/workshop-tutorials && \
    cd workshop-tutorials && \
    git remote rename origin gregcaporaso && \
    git remote add thermokarst https://github.com/thermokarst/workshop-tutorials && \
    git fetch thermokarst


### thermokarst
[src/thermokarst/ccdb-api]
checkout = git clone https://github.com/thermokarst/ccdb-api && \
    cd ccdb-api && \
    git remote rename origin thermokarst

[src/thermokarst/ccdb-web]
checkout = git clone https://github.com/thermokarst/ccdb-web && \
    cd ccdb-web && \
    git remote rename origin thermokarst

[src/thermokarst/fathm]
checkout = git clone https://github.com/thermokarst/fathm && \
    cd fathm && \
    git remote rename origin thermokarst && \
    git remote add gitlab https://gitlab.com/evalulogic/fathm.git && \
    git fetch gitlab

[src/thermokarst/tucotuco]
checkout = git clone https://github.com/thermokarst/tucotuco && \
    cd tucotuco && \
    git remote rename origin thermokarst