comparison run_segalign_diagonal_partition @ 4:36cafb694dd2 draft

planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/segalign commit b8aa943b38b865defab8a27e4404bb8a2131f919

3:6f46cebc9ed8

time {
    while IFS= read -r line; do
        "$TOOL_DIRECTORY/diagonal_partition.py" $MAX_SEGMENT_SIZE $line >> $LASTZ_COMMAND_FILE
        # segalign sort writes out the partitioned segment files to the working
        # directory and prints the modified lastz commands.
    done < <(stdbuf -oL segalign $ref_path $query_path "${DATA_FOLDER}/" "$@" ) # segalign begins running in this line, 
} 1>&2 # and every newline written to stdout, get assigned to $line which
       # gets sent to diagonal_partition for diagonal partitioning

4:36cafb694dd2

time {
    while IFS= read -r line; do
        python "$TOOL_DIRECTORY/diagonal_partition.py" $MAX_SEGMENT_SIZE $line >> $LASTZ_COMMAND_FILE
        # segalign sort writes out the partitioned segment files to the working
        # directory and prints the modified lastz commands.
    done < <(stdbuf -oL segalign $ref_path $query_path "${DATA_FOLDER}/" "$@" ) # segalign begins running in this line, 
} 1>&2 # and every newline written to stdout, get assigned to $line which
       # gets sent to diagonal_partition for diagonal partitioning