From 01219c00a4215259482dea0da4a6c41d86a34f4a Mon Sep 17 00:00:00 2001
From: Remy Schwab <rschwab8@gmail.coml>
Date: Fri, 26 May 2017 16:19:19 -0400
Subject: [PATCH] fixed index fetcher

---
 .DS_Store         | Bin 6148 -> 6148 bytes
 R/cn_preprocess.R |  22 ++++++++++------------
 2 files changed, 10 insertions(+), 12 deletions(-)

diff --git a/.DS_Store b/.DS_Store
index 5008ddfcf53c02e82d7eee2e57c38e5672ef89f6..e4593c008d867e8510f8de0d82fe47bc7e8cfd69 100644
GIT binary patch
delta 319
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zvZR5*bw(y;7FITP4o*%EPF{}K;Eeq8;F83W(qgB?qG&KLGbJ?%$_~lT&w;ZOlfp7n
z%i{$^ob&Ta5;OBsi;$GZglFcZ<d-|;mjbC`ut5QdB^f}?V4LCvB&w?|4UBXYjLnT|
zbrh=2%?)%EOpMKHYdJW?RSj)D6LKr7s%vWNW&*te1dKqBfdN01hEcPC3`T~avf!e;
wocz3W5N~55AKPRD5thx|9NZkh;Mth?oq009h$1T}926!SiU@D^5ZS{F0LiLS`2YX_

delta 70
zcmZoMXfc=|#>AjHu~2NHo+1YW5HK<@2yA9#Vq@DZz_f~SGdl-A2T%b}<U8|Zei21Z
TpgcnYNa17?9_7t3A}g2y-|-DD

diff --git a/R/cn_preprocess.R b/R/cn_preprocess.R
index 806699f..5a11b1a 100644
--- a/R/cn_preprocess.R
+++ b/R/cn_preprocess.R
@@ -103,23 +103,21 @@ fetchIndexHandler <- function
 #'
 #' @return nothing
 #' @export
-fetch_salmon_indices<-function
-(destination = "/media/ephemeral1/dat/ref", 
-  species = "mouse",
-  bucket = "cellnet-rnaseq",
-  dir = "ref",
-  iFile = "salmon.index.mouse.050316.tgz") 
+fetch_salmon_indices = function (destination = "/media/ephemeral1/dat/ref", species = "mouse", 
+          bucket = "cellnet-rnaseq", dir = "ref", iFile) 
 {
   curdir <- system("pwd", intern = T)
   setwd(destination)
-  fname2 <- iFile
   if (species == "mouse") {
+    fname2 = "salmon.index.mouse.050316.tgz"
     fname3 <- "geneToTrans_Mus_musculus.GRCm38.80.exo_Jun_02_2015.R"
-    fname4 <- "Mus_musculus.GRCm38.83.gtf.gz"
   }
   else {
+    fname2 = "salmon.index.human.050316.tgz"
     fname3 <- "geneToTrans_Homo_sapiens.GRCh38.80.exo_Jul_04_2015.R"
-    fname4 <- "Homo_sapiens.GRCh38.83.gtf.gz"
+  }
+  if(length(iFile) != 0) {
+    fname2 = iFile
   }
   cat("fetching and unpacking stuff needed for Salmon ...\n")
   pref <- paste0("https://s3.amazonaws.com/", bucket, "/", 
@@ -128,9 +126,9 @@ fetch_salmon_indices<-function
   cmd <- paste("tar zxvf ", fname2, sep = "")
   system(cmd)
   download.file(paste0(pref, fname3), destfile = fname3)
-  download.file(paste0(pref, fname4), destfile = fname4)
-  cmd <- paste("gzip -d ", fname4, sep = "")
-  system(cmd)
+  #download.file(paste0(pref, fname4), destfile = fname4)
+  #cmd <- paste("gzip -d ", fname4, sep = "")
+  system("rm *.tgz")
   setwd(curdir)
 }