cleanup perl/INSTALL.md; remove temp_dir by default; remove .zip hand…

…ling which won't work when libdeflate is used or bgzip is used
akotlar · Sep 18, 2024 · 15a84b1 · 15a84b1
1 parent 7bb6e12
commit 15a84b1
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Showing 7 changed files with 195 additions and 67 deletions.
diff --git a/config/hg19.yml b/config/hg19.yml
@@ -47,7 +47,7 @@ statistics:
   programPath: bystro-stats
   refTrackField: ref
   siteTypeField: refSeq.siteType
-temp_dir: /mnt/annotator/tmp
+temp_dir: ~
 tracks:
   outputOrder:
     - ref

diff --git a/config/hg38.yml b/config/hg38.yml
@@ -47,7 +47,7 @@ statistics:
   programPath: bystro-stats
   refTrackField: ref
   siteTypeField: refSeq.siteType
-temp_dir: /mnt/annotator/tmp
+temp_dir: ~
 tracks:
   outputOrder:
     - ref

diff --git a/install/install-go.sh b/install/install-go.sh
@@ -5,13 +5,13 @@ set -e
 
 # Ensure that DIR and PROFILE_FILE are provided
 if [ "$#" -ne 6 ]; then
-    echo "Usage: $0 <PROFILE_FILE> <GOPATH_PARENT_DIR> <GO_INSTALL_DIR> <BYSTRO_INSTALL_DIR> <GO_PLATFORM> <GO_VERSION>"
+    echo "Usage: $0 <PROFILE_FILE> <GOLANG_INSTALL_DIR> <BYSTRO_GO_PROGRAMS_INSTALL_DIR> <BYSTRO_INSTALL_DIR> <GO_PLATFORM> <GO_VERSION>"
     exit 1
 fi
 
 PROFILE_FILE="$1"
-GOPATH_PARENT_DIR="$2"
-INSTALL_DIR="$3"
+INSTALL_DIR="$2"
+GOPATH_PARENT_DIR="$3"
 BYSTRO_INSTALL_DIR="$4"
 GO_PLATFORM="$5"
 GO_VERSION="$6"

diff --git a/perl/INSTALL.md b/perl/INSTALL.md
diff --git a/perl/lib/Interface.pm b/perl/lib/Interface.pm
@@ -96,7 +96,7 @@ has compress => (
   is            => 'ro',
   isa           => 'Str',
   metaclass     => 'Getopt',
-  documentation => 'Compress the output?',
+  documentation => 'Enable compression. Specify the type of compression: lz4 gz bgz. `bgz` is an alias for gz (gzip); when bgzip is available, it will be used and will generate a block gzipped file with index',
   default       => 0,
 );
 

diff --git a/perl/lib/Seq/Definition.pm b/perl/lib/Seq/Definition.pm
@@ -47,7 +47,7 @@ has temp_dir => ( is => 'ro', isa => 'Maybe[Str]' );
 has compress => ( is => 'ro', isa => 'Str', default => 1 );
 
 has compressType =>
-  ( is => 'ro', isa => enum( [qw/lz4 gz bgz zip/] ), default => 'gz' );
+  ( is => 'ro', isa => enum( [qw/lz4 gz bgz/] ), default => 'gz' );
 
 # Do we want to tarball our results
 has archive => ( is => 'ro', isa => 'Bool', default => 0 );

diff --git a/perl/lib/Seq/Role/IO.pm b/perl/lib/Seq/Role/IO.pm
@@ -160,7 +160,6 @@ sub getInnerFileCommand {
   my $compressed =
        $innerFile =~ /[.]gz$/
     || $innerFile =~ /[.]bgz$/
-    || $innerFile =~ /[.]zip$/
     || $filePath  =~ /[.]lz4$/;
 
   my $innerCommand;
@@ -204,7 +203,7 @@ sub isCompressedSingle {
     return 0;
   }
 
-  if ( $basename =~ /[.]gz$/ || $basename =~ /[.]bgz$/ || $basename =~ /[.]zip$/ ) {
+  if ( $basename =~ /[.]gz$/ || $basename =~ /[.]bgz$/ ) {
     return "gzip";
   }
 
@@ -251,7 +250,7 @@ sub getWriteFh {
   }
 
   my $fh;
-  my $hasGz  = $file =~ /[.]gz$/ || $file =~ /[.]bgz$/ || $file =~ /[.]zip$/;
+  my $hasGz  = $file =~ /[.]gz$/ || $file =~ /[.]bgz$/;
   my $hasLz4 = $file =~ /[.]lz4$/;
   if ( $hasGz || $hasLz4 || $compress ) {
     if ( $hasLz4 || ( $compress && $compress =~ /[.]lz4$/ ) ) {