Unverified Commit 45790b3f authored by mvdbeek's avatar mvdbeek
Browse files

Let pysam use extra threads available in job

parent 50b62acc

lib/galaxy/datatypes/binary.py

+5 −3
Original line number Diff line number Diff line
@@ -930,11 +930,12 @@ class Bam(BamNative): 
            index_file = dataset.metadata.spec[spec_key].param.new_file(

                dataset=dataset, metadata_tmp_files_dir=metadata_tmp_files_dir

            )

        extra_threads = int(os.environ.get("GALAXY_SLOTS", 1)) - 1

        if index_flag == "-b":

            # IOError: No such file or directory: '-b' if index_flag is set to -b (pysam 0.15.4)

            pysam.index("-o", index_file.get_file_name(), dataset.get_file_name())  # type: ignore[attr-defined, unused-ignore]

            pysam.index("-o", index_file.get_file_name(), f"-@{extra_threads}", dataset.get_file_name())  # type: ignore[attr-defined, unused-ignore]

        else:

            pysam.index(index_flag, "-o", index_file.get_file_name(), dataset.get_file_name())  # type: ignore[attr-defined, unused-ignore]

            pysam.index(index_flag, "-o", index_file.get_file_name(), f"-@{extra_threads}", dataset.get_file_name())  # type: ignore[attr-defined, unused-ignore]

        dataset.metadata.bam_index = index_file



    def sniff(self, filename: str) -> bool:
@@ -1124,8 +1125,9 @@ class CRAM(Binary): 
            return -1, -1



    def set_index_file(self, dataset: HasFileName, index_file) -> bool:

        extra_threads = int(os.environ.get("GALAXY_SLOTS", 1)) - 1

        try:

            pysam.index("-o", index_file.get_file_name(), dataset.get_file_name())  # type: ignore[attr-defined, unused-ignore]

            pysam.index("-o", index_file.get_file_name(), f"-@{extra_threads}", dataset.get_file_name())  # type: ignore[attr-defined, unused-ignore]

            return True

        except Exception as exc:

            log.warning("%s, set_index_file Exception: %s", self, exc)