Mercurial > repos > richard-burhans > segalign

changeset 7:39c21be8f8b9 draft

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planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/segalign commit a87a48f823756ba950e9c87593342cfb90570e7b
author richard-burhans
date Tue, 07 May 2024 15:28:36 +0000
parents 6c95c380bfa7
children 150de8a3954a
files run_segalign_diagonal_partition
diffstat 1 files changed, 6 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/run_segalign_diagonal_partition	Mon May 06 17:44:50 2024 +0000
+++ b/run_segalign_diagonal_partition	Tue May 07 15:28:36 2024 +0000
@@ -80,11 +80,11 @@
 ##
 ## convert target and query to 2bit
 ##
-faToTwoBit "$ref_path" "$DATA_FOLDER/ref.2bit" || {
+faToTwoBit <(gzip -cdfq "$ref_path") "$DATA_FOLDER/ref.2bit" || {
     echo "run_segalign_diagonal_partition: cannot convert \"$ref_path\" to 2bit" 1>&2
     exit 1
 }
-faToTwoBit "$query_path" "$DATA_FOLDER/query.2bit" || {
+faToTwoBit <(gzip -cdfq "$query_path") "$DATA_FOLDER/query.2bit" || {
     echo "run_segalign_diagonal_partition: cannont convert \"$ref_path\" to 2bit" 1>&2
     exit 1
 }
@@ -93,7 +93,10 @@
 
 time {
     while IFS= read -r line; do
-        python "$TOOL_DIRECTORY/diagonal_partition.py" $MAX_SEGMENT_SIZE $line >> $LASTZ_COMMAND_FILE
+        python "$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,