FileConverter fails for symlinked raw input

[bernt-matthias]

For instance this test

OpenMS/src/tests/topp/THIRDPARTY/third_party_tests.cmake

Line 250 in 17a07f8

add_test("TOPP_THERMORAWFILEPARSER_1" ${TOPP_BIN_PATH}/FileConverter -test -in ${DATA_DIR_TOPP}/THIRDPARTY/ginkgotoxin-ms-switching.raw -ThermoRaw_executable "${THERMORAWFILEPARSER_BINARY}" -out ginkgotoxin-ms-switching_out_tmp.mzML)

if the input is a link.

Consequence is that for the Galaxy tools we can't use symlinks for the input data.

[jpfeuffer]

This is a problem with ThermoRawFileParser: compomics/ThermoRawFileParser#46

[jpfeuffer]

compomics/ThermoRawFileParser#108

[bernt-matthias]

Thanks for the link. Seems that this should be solved in recent versions compomics/ThermoRawFileParser#146

[jpfeuffer]

Yep. Not sure if we include the newest version in our conda thirdparty.

Unfortunately we are having major issues updating our thirdparty due to size limitations on mulled container tests. So, we will not be able to update them in the foreseeable future and might need to drop the thirdparty package.

[bernt-matthias]

Yep. Seems to be still a problem with the latest version compomics/ThermoRawFileParser#180