From 765311275526bbeeabc430ec09be81346f8c132e Mon Sep 17 00:00:00 2001
From: Yohan Jarosz <yohanjarosz@yahoo.fr>
Date: Thu, 2 Apr 2015 15:42:01 +0200
Subject: [PATCH] Softlinking prokka db next to binary :(
---
rules/Util.rules | 18 ++++++++++++++----
1 file changed, 14 insertions(+), 4 deletions(-)
diff --git a/rules/Util.rules b/rules/Util.rules
index d90a7b1..a90b49e 100644
--- a/rules/Util.rules
+++ b/rules/Util.rules
@@ -35,14 +35,24 @@ rule _DOWNLOAD_PROKKA_DATABASES:
expand("{path}/{db}", path=DBPATH, db=config["prokka"]["databases"])
shell:
"""
+ ### prokka by default will look databases where is located the binary.
+ ### we have to softlink to put the binary somewhere and the databases somewhere else.
+ if [[ "{DBPATH}" = /* ]]
+ then
+ PP={DBPATH};
+ else
+ PP=$PWD/{DBPATH};
+ fi
+ cd $(dirname $(which prokka))/.. && ln -s $PP db
+ echo "Softlinking $(dirname $(which prokka))/../db to $PP"
TMPDIR=$(mktemp -d -t "XXXXXX")
- wget {pkg_url} -O $TMPDIR/prokka.tgz
+ wget {config[prokka][pkg_url]} -O $TMPDIR/prokka.tgz
tar -xzf $TMPDIR/prokka.tgz --strip-components=1 -C $TMPDIR
- mkdir -p {path}
- cp -r $TMPDIR/db/* {path}/.
+ mkdir -p {DBPATH}
+ cp -r $TMPDIR/db/* {DBPATH}/.
rm -rf $TMPDIR
prokka --setupdb
- """.format(pkg_url=config["prokka"]["pkg_url"], path=DBPATH)
+ """
rule _DOWNLOAD_TRIMMOMATIC_ADAPTERS:
--
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