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Merge pull request #699 from jmchilton/doc_tests
Implement some ad-hoc documentation tests.
2 parents 44317f4 + 4209bee commit c92eb2c

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‎docs/_writing_testing.rst

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@@ -10,7 +10,7 @@ install BWA - but however you obtain it should be fine.
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::
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$ conda install -c bioconda bwa
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$ conda install --force -c bioconda bwa
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... bwa installation ...
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$ bwa
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Program: bwa (alignment via Burrows-Wheeler transformation)

‎docs/_writing_using_seqtk.rst

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@@ -7,7 +7,7 @@ install Seqtk - but however you obtain it should be fine.
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::
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$ conda install -c bioconda seqtk=1.2
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$ conda install --force -c bioconda seqtk=1.2
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... seqtk installation ...
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$ seqtk seq
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Usage: seqtk seq [options] <in.fq>|<in.fa>

‎docs/tests/tests_all.sh

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#!/bin/bash
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set -o xtrace
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set -e
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DOC_TESTS_DIRECTORY="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
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bash "${DOC_TESTS_DIRECTORY}/tests_building.sh"
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bash "${DOC_TESTS_DIRECTORY}/tests_tdd.sh"
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bash "${DOC_TESTS_DIRECTORY}/tests_conda.sh"
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bash "${DOC_TESTS_DIRECTORY}/tests_docker.sh"

‎docs/tests/tests_building.sh

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#!/bin/bash
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set -o xtrace
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set -e
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# Preconditions - tool init directory doesn't exist and in home directory.
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cd
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rm -rf tool_init_exercise
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# Tests
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conda install --force -c bioconda seqtk=1.2
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seqtk seq
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mkdir tool_init_exercise
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cd tool_init_exercise
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wget https://raw.githubusercontent.com/galaxyproject/galaxy-test-data/master/2.fastq
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seqtk seq -A 2.fastq > 2.fasta
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cat 2.fasta
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planemo tool_init --id 'seqtk_seq' --name 'Convert to FASTA (seqtk)'
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cat seqtk_seq.xml
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planemo tool_init --force \
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--id 'seqtk_seq' \
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--name 'Convert to FASTA (seqtk)' \
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--requirement [email protected] \
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--example_command 'seqtk seq -a 2.fastq > 2.fasta' \
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--example_input 2.fastq \
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--example_output 2.fasta
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cat seqtk_seq.xml
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planemo tool_init --force \
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--id 'seqtk_seq' \
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--name 'Convert to FASTA (seqtk)' \
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--requirement [email protected] \
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--example_command 'seqtk seq -a 2.fastq > 2.fasta' \
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--example_input 2.fastq \
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--example_output 2.fasta \
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--test_case \
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--cite_url 'https://github.com/lh3/seqtk' \
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--help_from_command 'seqtk seq'
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planemo l
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planemo t
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planemo shed_init --name=seqtk_seq \
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--owner=planemo \
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--description=seqtk_seq \
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--long_description="Tool that converts FASTQ to FASTA files using seqtk" \
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--category="Fastq Manipulation"
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planemo shed_lint --tools
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planemo shed_create --shed_target local
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planemo shed_update --shed_target local
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planemo tool_init --force \
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--macros \
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--id 'seqtk_seq' \
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--name 'Convert to FASTA (seqtk)' \
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--requirement [email protected] \
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--example_command 'seqtk seq -A 2.fastq > 2.fasta' \
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--example_input 2.fastq \
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--example_output 2.fasta \
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--test_case \
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--help_from_command 'seqtk seq'
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cat seqtk_seq.xml
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‎docs/tests/tests_conda.sh

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#!/bin/bash
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set -o xtrace
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set -e
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shopt -s expand_aliases # Needed for conda_env test
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# Preconditions:
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# - seqtk_example doesn't exist and in home directory
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# - conda_exercises doesn't exist in home directory.
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# - seqtk environment is absent
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cd
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rm -rf seqtk_example
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rm -rf conda_exercises
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echo "Remove existing seqtk environment - it is fine if it doesn't exist."
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conda remove --force --name '[email protected]' --all || true
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# Tests
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echo "Try planemo conda_init - this may fail and will always fail on planemo-machine"
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echo "still good to see a decent error message though."
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planemo conda_init || true
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echo "Setup completed seqtk example"
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planemo project_init --template=seqtk_complete seqtk_example
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cd seqtk_example
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echo "Check conda_requirements - should see them linting properly"
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planemo lint --conda_requirements seqtk_seq.xml
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planemo conda_install seqtk_seq.xml
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echo "Checking for seqtk - shouldn't be present"
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which seqtk || true
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echo "Simulating '. <(planemo conda_env seqtk_seq.xml)', subshell-ism doesn't seem to work in script"
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planemo conda_env seqtk_seq.xml > .conda_env
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. .conda_env
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echo "Inside conda_env I should see seqtk"
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which seqtk
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conda_env_deactivate
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sleep 5 # Need to wait for the package to get cleaned up.
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planemo test seqtk_seq.xml
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echo "Doing a search - should see seqtk in bioconda results along with versions"
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planemo conda_search seqt
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cd
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planemo project_init --template conda_exercises conda_exercises
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cd conda_exercises/exercise_1
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ls
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echo "Running test wrong - this should fail"
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planemo test pear.xml || true
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echo "Linting pear without requirements - this should fail"
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planemo lint --conda_requirements pear.xml || true
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echo "Should see pear from bioconda at 0.9.6"
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planemo conda_search pear
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wget https://raw.githubusercontent.com/galaxyproject/planemo/master/project_templates/conda_answers/exercise_1/pear.xml -O pear.xml
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planemo lint --conda_requirements pear.xml || true
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planemo test pear.xml
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cd ../exercise_2
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# Fetch and build recipe.
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mkdir fleeqtk
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cd fleeqtk
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wget https://raw.githubusercontent.com/galaxyproject/planemo/master/project_templates/conda_answers/exercise_2/fleeqtk/build.sh
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wget https://raw.githubusercontent.com/galaxyproject/planemo/master/project_templates/conda_answers/exercise_2/fleeqtk/meta.yaml
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cd ..
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conda build fleeqtk
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# Update to fix tool and see it work.
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wget https://raw.githubusercontent.com/galaxyproject/planemo/master/project_templates/conda_answers/exercise_2/fleeqtk_seq.xml -O fleeqtk_seq.xml
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planemo conda_install --conda_use_local fleeqtk_seq.xml
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planemo test fleeqtk_seq.xml

‎docs/tests/tests_docker.sh

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#!/bin/bash
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set -o xtrace
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set -e
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# Preconditions - seqtk_example directory doesn't exist and in home directory.
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cd
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rm -rf seqtk_example
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rm -rf conda_testing
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echo "Setup completed seqtk example"
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planemo project_init --template=seqtk_complete seqtk_example
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cd seqtk_example
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echo "We should see biocontainer found for this tool"
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planemo lint --biocontainers seqtk_seq.xml
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echo "This should pass and we should see container was used."
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planemo test --biocontainers seqtk_seq.xml
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cd ..
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planemo project_init --template=conda_testing conda_testing
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cd conda_testing/
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echo "Should show quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:03dc1d2818d9de56938078b8b78b82d967c1f820-0 is built"
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planemo mull bwa_and_samtools.xml
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echo "Should see quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:03dc1d2818d9de56938078b8b78b82d967c1f820-0. "
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docker images
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echo "Should see cached container was used for this"
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planemo test --biocontainers bwa_and_samtools.xml

‎docs/tests/tests_tdd.sh

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#!/bin/bash
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set -o xtrace
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set -e
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# Preconditions - bwa directory doesn't exist and in home directory.
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cd
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rm -rf bwa
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# Tests
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conda install -c bioconda bwa
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echo "Executing bwa to see help - should see output, but it has a non-zero exit code."
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bwa | true
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planemo project_init --template bwa bwa
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cd bwa
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cd test-data
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bwa index -a is bwa-mem-mt-genome.fa
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bwa mem bwa-mem-mt-genome.fa bwa-mem-fastq1.fq bwa-mem-fastq2.fq | \
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samtools view -Sb - > temporary_bam_file.bam && \
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(samtools sort -f temporary_bam_file.bam bwa-aln-test2.bam || samtools sort -o bwa-aln-test2.bam temporary_bam_file.bam)
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cd ..
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wget https://raw.githubusercontent.com/galaxyproject/planemo/master/docs/writing/bwa-mem_v2.xml -O bwa-mem.xml
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echo "Running test we expect to fail..."
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planemo t || true
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echo "Fixing tool"
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wget https://raw.githubusercontent.com/galaxyproject/planemo/master/docs/writing/bwa-mem_v3.xml -O bwa-mem.xml
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echo "Running test we expect to be fixed."
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planemo t --failed
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# TODO: Finish remaining BWA examples if time.

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