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v4.3.7 #12

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merged 12 commits into from
Oct 10, 2024
Merged

v4.3.7 #12

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e0bb7b6
init changes
antgonza Oct 8, 2024
f4c38b6
rRNA_databases
antgonza Oct 8, 2024
0bec68e
testing folder
antgonza Oct 8, 2024
ccffcf2
QIITA_ROOTCA_CERT
antgonza Oct 8, 2024
6b4fbbd
adding new commands
antgonza Oct 8, 2024
7297d62
QiitaClient
antgonza Oct 8, 2024
d991141
renaming files
antgonza Oct 9, 2024
e616780
adding logs
antgonza Oct 9, 2024
456e19f
.ribosomal.R1.log -> .log
antgonza Oct 10, 2024
c10be82
1g
antgonza Oct 10, 2024
0815b4a
resources
antgonza Oct 10, 2024
e1ad0fc
time
antgonza Oct 10, 2024
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19 changes: 11 additions & 8 deletions .github/workflows/qiita-plugin-ci.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -70,7 +70,7 @@ jobs:
shell: bash -l {0}
run: |
conda activate qiita
export QIITA_SERVER_CERT=`pwd`/qiita-dev/qiita_core/support_files/server.crt
export QIITA_ROOTCA_CERT=`pwd`/qiita-dev/qiita_core/support_files/server.crt
export QIITA_CONFIG_FP=`pwd`/qiita-dev/qiita_core/support_files/config_test.cfg
pip install qiita-dev/ --no-binary redbiom
mkdir ~/.qiita_plugins
Expand All @@ -81,22 +81,25 @@ jobs:
conda config --add channels anaconda
conda config --add channels conda-forge
conda config --add channels bioconda
conda create -q --yes -n qp-meta python=3.9 biom-format sortmerna=2.1b samtools pigz
conda create -q --yes -n qp-meta python=3.9 biom-format sortmerna=4.3.7 samtools pigz
conda activate qp-meta

export QIITA_SERVER_CERT=`pwd`/qiita-dev/qiita_core/support_files/ci_rootca.crt
export QIITA_ROOTCA_CERT=`pwd`/qiita-dev/qiita_core/support_files/ci_rootca.crt
export QIITA_CONFIG_FP=`pwd`/qiita-dev/qiita_core/support_files/config_test_local.cfg

pip --quiet install -U pip
pip --quiet install .
pip --quiet install coveralls

export QC_SORTMERNA_DB_DP=$PWD/qp_meta/sortmerna/databases/rRNA_databases/
export QC_SORTMERNA_DB_DP=$PWD/qp_meta/sortmerna/
pushd $QC_SORTMERNA_DB_DP
for file in $(ls); do gunzip $file; done
mkdir -p databases/rRNA_databases/
cd databases/rRNA_databases/
wget https://github.com/sortmerna/sortmerna/releases/download/v4.3.4/database.tar.gz
tar zxvf database.tar.gz
popd

configure_meta --env-script "source /home/runner/.profile; conda activate qp-meta; export QC_SORTMERNA_DB_DP=$PWD/qp_meta/sortmerna/databases/rRNA_databases/; export ENVIRONMENT=\"source /home/runner/.profile; conda activate qp-meta\"" --server-cert $QIITA_SERVER_CERT
configure_meta --env-script "source /home/runner/.profile; conda activate qp-meta; export QC_SORTMERNA_DB_DP=$PWD/qp_meta/sortmerna/databases/rRNA_databases/; export ENVIRONMENT=\"source /home/runner/.profile; conda activate qp-meta\"" --server-cert $QIITA_ROOTCA_CERT

echo "Available Qiita plugins"
ls ~/.qiita_plugins/
Expand All @@ -106,7 +109,7 @@ jobs:
shell: bash -l {0}
run: |
conda activate qiita
export QIITA_SERVER_CERT=`pwd`/qiita-dev/qiita_core/support_files/ci_rootca.crt
export QIITA_ROOTCA_CERT=`pwd`/qiita-dev/qiita_core/support_files/ci_rootca.crt
export QIITA_CONFIG_FP=`pwd`/qiita-dev/qiita_core/support_files/config_test_local.cfg
sed "s#/home/runner/work/qiita/qiita#${PWD}/qiita-dev/#g" `pwd`/qiita-dev/qiita_core/support_files/config_test.cfg > ${QIITA_CONFIG_FP}

Expand Down Expand Up @@ -139,7 +142,7 @@ jobs:
run: |
conda activate qp-meta

export QIITA_SERVER_CERT=`pwd`/qiita-dev/qiita_core/support_files/ci_rootca.crt
export QIITA_ROOTCA_CERT=`pwd`/qiita-dev/qiita_core/support_files/ci_rootca.crt
export QIITA_CONFIG_FP=`pwd`/qiita-dev/qiita_core/support_files/config_test_local.cfg
export QC_SORTMERNA_DB_DP=$PWD/qp_meta/sortmerna/databases/rRNA_databases/
export ENVIRONMENT="source /home/runner/.profile; conda activate qp-meta"
Expand Down
14 changes: 3 additions & 11 deletions qp_meta/sortmerna/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -14,24 +14,16 @@

# Defining the Sortmerna command
req_params = {'input': ('artifact', ['per_sample_FASTQ'])}
opt_params = {
'Output blast format': ['integer', '1'],
'Number of alignments': ['integer', '1'],
'Memory': ['integer', '3988']
}
opt_params = {}
outputs = {'Non-ribosomal reads': 'per_sample_FASTQ',
'Ribosomal reads': 'per_sample_FASTQ'}

# defining default parameter set AKA what's going to be shown to the user
# as options for the command
dflt_param_set = {
'Ribosomal read filtering': {
'Output blast format': 1,
'Number of alignments': 1,
'Memory': 31000
}
'Ribosomal read filtering': {}
}

sortmerna_cmd = QiitaCommand(
'Sortmerna v2.1b', "Ribosomal read filtering", sortmerna,
'SortMeRNA v4.3.7', "Ribosomal read filtering", sortmerna,
req_params, opt_params, outputs, dflt_param_set)
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