From 4ec729c799bb2a14fe69c1248d759988133a5c30 Mon Sep 17 00:00:00 2001
From: peterjc <p.j.a.cock@googlemail.com>
Date: Fri, 19 Oct 2018 16:50:10 +0100
Subject: [PATCH] Workaround for gzip support breaking on Galaxy 16.01

See https://github.com/galaxyproject/tools-iuc/issues/1373
which was fixed and back-ported to Galaxy 16.07,
https://github.com/galaxyproject/galaxy/pull/4224
https://github.com/galaxyproject/galaxy/pull/4230

This would still break with other non-compressed FASTA
subclasses, but this is intended as a stop-gap until
the last few elderly Galaxy servers in use are updated.
---
 tools/ncbi_blast_plus/ncbi_macros.xml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tools/ncbi_blast_plus/ncbi_macros.xml b/tools/ncbi_blast_plus/ncbi_macros.xml
index 829f74b1..0c55fabb 100644
--- a/tools/ncbi_blast_plus/ncbi_macros.xml
+++ b/tools/ncbi_blast_plus/ncbi_macros.xml
@@ -567,7 +567,7 @@
     <token name="@THREADS@">-num_threads "\${GALAXY_SLOTS:-8}"</token>
 
     <token name="@QUERY@"><![CDATA[
-#if $query.is_of_type('fasta.gz'):
+#if $query.is_of_type('fasta.gz') and $query.ext != "fasta":
   -query <(gunzip -c '${query}')
 #else:
   -query '${query}'
@@ -580,7 +580,7 @@
 #elif $db_opts.db_opts_selector == "histdb":
   -db '${os.path.join($db_opts.histdb.extra_files_path, "blastdb")}'
 #else:
-    #if $db_opts.subject.is_of_type('fasta.gz'):
+    #if $db_opts.subject.is_of_type('fasta.gz') and $db_opts.subject.ext != "fasta":
         -subject <(gunzip -c '${$db_opts.subject}')
     #else:
         -subject '${db_opts.subject}'