Fix sra-tools file_list mode

galaxyproject · Jul 1, 2020 · ec1cc6c0c290e9931780ea128bb48caac37977db · ec1cc6c
1 parent 1e2492f
commit ec1cc6c0c290e9931780ea128bb48caac37977db
Showing with 4 additions and 4 deletions.

+1 −1 tools/sra-tools/fasterq_dump.xml

+1 −1 tools/sra-tools/fastq_dump.xml

+1 −1 tools/sra-tools/sam_dump.xml

+1 −1 tools/sra-tools/sra_macros.xml
diff --git a/tools/sra-tools/fasterq_dump.xml b/tools/sra-tools/fasterq_dump.xml
@@ -1,4 +1,4 @@
-<tool id="fasterq_dump" name="Faster Download and Extract Reads in FASTQ" version="@VERSION@+galaxy1" profile="18.01">
+<tool id="fasterq_dump" name="Faster Download and Extract Reads in FASTQ" version="@VERSION@+galaxy2" profile="18.01">
     <description>format from NCBI SRA</description>
     <macros>
         <import>sra_macros.xml</import>

diff --git a/tools/sra-tools/fastq_dump.xml b/tools/sra-tools/fastq_dump.xml
@@ -1,4 +1,4 @@
-<tool id="fastq_dump" name="Download and Extract Reads in FASTA/Q" version="@VERSION@+galaxy1" profile="18.01">
+<tool id="fastq_dump" name="Download and Extract Reads in FASTA/Q" version="@VERSION@+galaxy2" profile="18.01">
     <description>format from NCBI SRA</description>
     <macros>
         <import>sra_macros.xml</import>

diff --git a/tools/sra-tools/sam_dump.xml b/tools/sra-tools/sam_dump.xml
@@ -1,4 +1,4 @@
-<tool id="sam_dump" name="Download and Extract Reads in BAM" version="@VERSION@+galaxy1" profile="18.01">
+<tool id="sam_dump" name="Download and Extract Reads in BAM" version="@VERSION@+galaxy2" profile="18.01">
     <description>format from NCBI SRA</description>
     <macros>
         <import>sra_macros.xml</import>

diff --git a/tools/sra-tools/sra_macros.xml b/tools/sra-tools/sra_macros.xml
@@ -23,7 +23,7 @@
                 #set $column = $input.file_list.unsanitized.metadata.column_names.index('Run') + 1
                 cut -f $column '$input.file_list'| tail -n +2 > "manifest" &&
             #else
-                ln -s '$input.file_list' > manifest &&
+                ln -s '$input.file_list' manifest &&
             #end if
             for acc in `@ACCESSIONS_FROM_FILE@ manifest` ;
             do (