# HG changeset patch
# User galaxyp
# Date 1495067019 14400
# Node ID 2cba79e6037e691a1566bc8039249c7409709f49
# Parent  ad130eaa3a05982dad6888b4809f8981dbef9338
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb

diff -r ad130eaa3a05 -r 2cba79e6037e customProDB.R
--- a/customProDB.R	Fri May 12 13:17:40 2017 -0400
+++ b/customProDB.R	Wed May 17 20:23:39 2017 -0400
@@ -99,11 +99,6 @@
     file.symlink(bam_file, bamLink)
     file.symlink(bai_file, paste(bamLink, ".bai", sep=""))
 
-    # load from GitHub until conda package is available
-    download.file("https://github.com/ggrothendieck/sqldf/archive/master.zip", "sqldf.zip", quiet=TRUE)
-    unzip("sqldf.zip")
-    devtools::load_all("sqldf-master")
-
     # load customProDB from GitHub (NOTE: downloading the zip is faster than cloning the repo with git2r or devtools::install_github)
     download.file("https://github.com/chambm/customProDB/archive/master.zip", "customProDB.zip", quiet=TRUE)
     unzip("customProDB.zip")
diff -r ad130eaa3a05 -r 2cba79e6037e customProDB.xml
--- a/customProDB.xml	Fri May 12 13:17:40 2017 -0400
+++ b/customProDB.xml	Wed May 17 20:23:39 2017 -0400
@@ -14,7 +14,7 @@
     <requirement type="package" version="1.1.2">r-stringi</requirement>
     <requirement type="package" version="1.1.0">r-stringr</requirement>
     <requirement type="package" version="1.10.0">r-data.table</requirement>
-    <!--<requirement type="package" version="0.4_10">r-sqldf</requirement>-->
+    <requirement type="package" version="0.4_10">r-sqldf</requirement>
     <requirement type="package" version="0.6_6">r-gsubfn</requirement>
     <requirement type="package" version="2.3_47">r-chron</requirement>
     <requirement type="package" version="0.3.10">r-proto</requirement>
@@ -57,7 +57,7 @@
                 --cosmic='$index_path/cosmic.RData'
             #end if
        #end if
-       2>1
+    2>&1
 ]]>
   </command>
   <inputs>