minor upd

circos_tutorial.rst

@@ -2,6 +2,8 @@
 Using and Installing Circos
 ======================================
 
+.. https://s3-us-west-1.amazonaws.com/dib-training.ucdavis.edu/metagenomics-scripps-2016-10-12/circos-build.tar.gz
+
 Circos is a powerful visualization tool that allows for the creation of circular graphics to display complex genomic data (e.g. genome comparisons). On top of the circular ideogram generated can be layered any number of graphical information (heatmaps, scatter plots, etc.).
 
 The goals of this tutorial are to:

salmon_tutorial.rst

@@ -16,6 +16,7 @@ Installing Salmon
 
 Download and extract the latest version of Salmon and add it to your PATH:
 ::
+    cd
     wget https://github.com/COMBINE-lab/salmon/releases/download/v0.7.2/Salmon-0.7.2_linux_x86_64.tar.gz
     tar -xvzf Salmon-0.7.2_linux_x86_64.tar.gz
     cd Salmon-0.7.2_linux_x86_64
@@ -26,16 +27,17 @@ Running Salmon
 
 Go to the data directory and download the prokka annotated sequences, assembled metagenome, and fastq files:
 ::
+  mkdir -p /mnt/data
   cd /mnt/data
   curl -L -O https://s3-us-west-1.amazonaws.com/dib-training.ucdavis.edu/metagenomics-scripps-2016-10-12/SRR1976948.abundtrim.subset.pe.fq.gz
   curl -L -O https://s3-us-west-1.amazonaws.com/dib-training.ucdavis.edu/metagenomics-scripps-2016-10-12/SRR1977249.abundtrim.subset.pe.fq.gz
-  curl -L -O **** prokka_annotation_assembly.tar.gz ***
+  curl -L -O https://s3-us-west-1.amazonaws.com/dib-training.ucdavis.edu/metagenomics-scripps-2016-10-12/prokka_annotation_assembly.tar.gz
   tar -xvzf prokka_annotation_assembly.tar.gz
 
 Make a new directory for the quantification of data with Salmon:
 ::
     mkdir /mnt/quant
-    cd quant
+    cd /mnt/quant
 
 
 Grab the nucleotide (``*ffn``) predicted protein regions from Prokka and link them here. Also grab the trimmed sequence data (``*fq``)