comparison generate.sh @ 11:2c6f5858e89a draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"

10:a717bea32e41

#!/usr/bin/env bash

# VERSION=2.3
# CONDAPKG=https://anaconda.org/bioconda/openms/2.3.0/download/linux-64/openms-2.3.0-py27h932d754_3.tar.bz2
# VERSION=2.4
# CONDAPKG=https://anaconda.org/bioconda/openms/2.4.0/download/linux-64/openms-2.4.0-py27h574aadf_1.tar.bz2

VERSION=2.5
FILETYPES="filetypes.txt"
PROFILE="20.05"
## FILETYPES_RE=$(grep -v "^#" $FILETYPES | grep -v "^$" | cut -f 1 -d" " | tr '\n' '|' | sed 's/|$//'| sed 's/|/\\|/g')

export tmp=$(mktemp -d)

export CTDCONVERTER="$tmp/CTDConverter"

export PYTHONPATH="$(pwd)/CTDopts/"
###############################################################################
## reset old data
###############################################################################
# rm $(ls *xml |grep -v macros)
# rm -rf ctd

fi
# export PYTHONPATH=$(pwd)/CTDopts
###############################################################################
## conversion ctd->xml 
###############################################################################
source $(dirname $(which conda))/../etc/profile.d/conda.sh
conda activate $tmp/OpenMS$VERSION-env
python $CTDCONVERTER/convert.py galaxy -i ctd/*ctd -o ./ -s tools_blacklist.txt -f "$FILETYPES" -m macros.xml -t tool.conf  -p hardcoded_params.json --test-macros macros_autotest.xml --test-macros-prefix autotest_  --test-macros macros_test.xml --test-macros-prefix manutest_ --tool-version $VERSION --tool-profile $PROFILE > convert.out 2> convert.err
if [[ "$?" -ne "0" ]]; then >&2 echo 'CTD -> XML conversion failed'; >&2 echo -e "stderr:\n$(cat convert.err)"; fi
conda deactivate

patch PepNovoAdapter.xml < PepNovoAdapter.patch
patch OMSSAAdapter.xml < OMSSAAdapter.patch
patch -p0 <404-urls.patch

# #-b version log debug test in_type executable pepnovo_executable param_model_directory rt_concat_trafo_out param_id_pool

# for i in A-E F-H I-L M-N O-P Q-Z

11:2c6f5858e89a

#!/usr/bin/env bash

VERSION=2.6
FILETYPES="filetypes.txt"
PROFILE="20.05"
## FILETYPES_RE=$(grep -v "^#" $FILETYPES | grep -v "^$" | cut -f 1 -d" " | tr '\n' '|' | sed 's/|$//'| sed 's/|/\\|/g')

export tmp=$(mktemp -d)
export CTDCONVERTER="$tmp/CTDConverter"

###############################################################################
## reset old data
###############################################################################
# rm $(ls *xml |grep -v macros)
# rm -rf ctd

fi
# export PYTHONPATH=$(pwd)/CTDopts
###############################################################################
## conversion ctd->xml 
###############################################################################

find . -maxdepth 0 -name "[A-Z]*xml" -delete
source $(dirname $(which conda))/../etc/profile.d/conda.sh
conda activate $tmp/OpenMS$VERSION-env
python $CTDCONVERTER/convert.py galaxy -i ctd/*ctd -o ./ -s tools_blacklist.txt -f "$FILETYPES" -m macros.xml -t tool.conf  -p hardcoded_params.json --test-macros macros_autotest.xml --test-macros-prefix autotest_  --test-macros macros_test.xml --test-macros-prefix manutest_ --tool-version $VERSION --tool-profile $PROFILE > convert.out 2> convert.err
if [[ "$?" -ne "0" ]]; then >&2 echo 'CTD -> XML conversion failed'; >&2 echo -e "stderr:\n$(cat convert.err)"; fi
conda deactivate

patch PepNovoAdapter.xml < PepNovoAdapter.patch
patch OMSSAAdapter.xml < OMSSAAdapter.patch

# https://github.com/OpenMS/OpenMS/pull/4984
sed -i -e 's@http://www.openms.de/documentation/@http://www.openms.de/doxygen/release/2.6.0/html/@' ./*xml
# https://github.com/OpenMS/OpenMS/pull/4984#issuecomment-702641976
patch -p0 <404-urls.patch

# #-b version log debug test in_type executable pepnovo_executable param_model_directory rt_concat_trafo_out param_id_pool

# for i in A-E F-H I-L M-N O-P Q-Z