From 95264d1af5b48dad2d1f40552882ee3909bb6c68 Mon Sep 17 00:00:00 2001
From: Yohan Jarosz <yohanjarosz@yahoo.fr>
Date: Mon, 1 Jun 2015 14:28:49 +0200
Subject: [PATCH] should #fix 30
---
Snakefile | 22 ++++++++++++++++++++++
rules/Util.rules | 1 +
2 files changed, 23 insertions(+)
diff --git a/Snakefile b/Snakefile
index 86a6259..2036705 100644
--- a/Snakefile
+++ b/Snakefile
@@ -4,6 +4,7 @@ import gzip
import json
import bz2
from copy import deepcopy
+import subprocess
def dict_merge(a, b):
@@ -82,6 +83,27 @@ def prepare_environment(stepname):
return out, os.path.join(out, '%s.log' % stepname)
+def symlink_prokka():
+ # ## 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.
+ cmd = """
+ if [[ "{DBPATH}" = /* ]]
+ then
+ PP={DBPATH};
+ else
+ PP=$PWD/{DBPATH};
+ fi
+ DD=$(dirname $(which prokka))/../db
+ if [[ ! -L $DD ]]
+ then
+ echo "Softlinking $DD to $PP"
+ cd $(dirname $(which prokka))/.. && ln -s $PP db
+ fi
+ """
+ shell(cmd)
+
+symlink_prokka()
+
# INCLUDES RULES
include:
"rules/Util.rules"
diff --git a/rules/Util.rules b/rules/Util.rules
index 71c2cdb..d77387f 100644
--- a/rules/Util.rules
+++ b/rules/Util.rules
@@ -55,6 +55,7 @@ rule _DOWNLOAD_PROKKA_DATABASES:
"""
+
rule _DOWNLOAD_TRIMMOMATIC_ADAPTERS:
output:
"{DBPATH}/adapters/adapters.done"
--
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