From 6d68b1694ae8c0461f1fd3aa56caa714421dcaf3 Mon Sep 17 00:00:00 2001
From: cgpu <chatzipantsiou@gmail.com>
Date: Fri, 14 Feb 2020 18:15:08 +0000
Subject: [PATCH] Eliminates last install.packages() call; Adresses
 https://github.com/TheJacksonLaboratory/lifebitCloudOSDRE/issues/28

---
 jupyter/Figure1cYarnVersion.ipynb | 22 ++++++----------------
 1 file changed, 6 insertions(+), 16 deletions(-)

diff --git a/jupyter/Figure1cYarnVersion.ipynb b/jupyter/Figure1cYarnVersion.ipynb
index c59195c..fd552b5 100644
--- a/jupyter/Figure1cYarnVersion.ipynb
+++ b/jupyter/Figure1cYarnVersion.ipynb
@@ -11,7 +11,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Heatplot representing similarity in the fold-changes between male and female samples, with the values in the heatmap being the correlation between the vectors of fold changes of the tissues</b>"
+    "A `heatplot` representing similarity in the fold-changes between male and female samples, with the values in the heatmap being the correlation between the vectors of fold changes of the tissues. </b>"
    ]
   },
   {
@@ -25,18 +25,6 @@
     "merged related sub-tissues, performed tissue-aware normalization using qsmooth (Hicks et al, 2017)."
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# Capture bash command output in a variable\n",
-    "# StackOverflow find here: https://stackoverflow.com/questions/11098277/store-output-of-system-command-into-a-variable-in-r\n",
-    "condaenvs<-system(\"conda env list\", intern = TRUE)\n",
-    "condaenvs"
-   ]
-  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -54,7 +42,9 @@
     "library(readr)\n",
     "library(biomaRt)\n",
     "library(DBI) # v >= 1.1.0 required for biomaRt\n",
-    "library(devtools)"
+    "library(devtools)\n",
+    "library(yarn)\n",
+    "Sys.setenv(TAR = \"/bin/tar\") # for gzfile"
    ]
   },
   {
@@ -77,7 +67,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "library(yarn)\n",
+    "# CAUTION! It requires some minutes to complete, also memory and enough storage\n",
     "obj <- yarn::downloadGTExV8(type='genes',file='data/gtex.rds')"
    ]
   },
@@ -94,7 +84,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "summary(obj)"
+    "class(obj)"
    ]
   },
   {