comparison run_segalign_diagonal_partition @ 7:39c21be8f8b9 draft

planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/segalign commit a87a48f823756ba950e9c87593342cfb90570e7b

6:6c95c380bfa7

echo "Converting fasta files to 2bit format" 1>&2

##
## convert target and query to 2bit
##
faToTwoBit "$ref_path" "$DATA_FOLDER/ref.2bit" || {
    echo "run_segalign_diagonal_partition: cannot convert \"$ref_path\" to 2bit" 1>&2
    exit 1
}
faToTwoBit "$query_path" "$DATA_FOLDER/query.2bit" || {
    echo "run_segalign_diagonal_partition: cannont convert \"$ref_path\" to 2bit" 1>&2
    exit 1
}



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

7:39c21be8f8b9

echo "Converting fasta files to 2bit format" 1>&2

##
## convert target and query to 2bit
##
faToTwoBit <(gzip -cdfq "$ref_path") "$DATA_FOLDER/ref.2bit" || {
    echo "run_segalign_diagonal_partition: cannot convert \"$ref_path\" to 2bit" 1>&2
    exit 1
}
faToTwoBit <(gzip -cdfq "$query_path") "$DATA_FOLDER/query.2bit" || {
    echo "run_segalign_diagonal_partition: cannont convert \"$ref_path\" to 2bit" 1>&2
    exit 1
}



time {
    while IFS= read -r line; do
        python "$TOOL_DIRECTORY/diagonal_partition.py" $MAX_SEGMENT_SIZE $line >> $LASTZ_COMMAND_FILE || {
            echo "run_segalign_diagonal_partition: failed: diagonal_partition.py $MAX_SEGMENT_SIZE $line" 1>&2
            exit 1
        }
        # 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