diff generate.sh @ 13:ed9a839cbbda draft

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

--- a/generate.sh	Wed Sep 23 15:00:46 2020 +0000
+++ b/generate.sh	Tue Oct 13 20:10:05 2020 +0000
@@ -1,20 +1,13 @@
 #!/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
+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"
 
-export PYTHONPATH="$(pwd)/CTDopts/"
 ###############################################################################
 ## reset old data
 ###############################################################################
@@ -59,6 +52,8 @@
 ###############################################################################
 ## 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
@@ -67,6 +62,10 @@
 
 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