Merge branch 'master' into tr/links

ngs-docs · Nov 8, 2018 · 6d7b43f · 6d7b43f
2 parents 586e96d + 452b4f7
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diff --git a/docs/cicese-cluster.md b/docs/cicese-cluster.md
@@ -42,17 +42,6 @@ ssh <usuario>@omica.cicese.mx
 
 
 
-## Using the Installed Software
-
-To use the software we have previously installed you'll need to execute the following:
-
-```
-echo 'export PATH=/LUSTRE/apps/workshop/miniconda3/bin:$PATH' >> ~/.bashrc
-echo 'export PATH=/LUSTRE/apps/workshop/transrate-1.0.3-linux-x86_64:$PATH' >> ~/.bashrc
-source ~/.bashrc
-```
-
-
 ## Working on the cluster
 
 After logging in, make sure to switch to a node:
@@ -69,6 +58,17 @@ Now, to enter our `conda` environment, run:
 source activate tara
 ```
 
+## Setting up the environment
+
+To set up the software we have previously installed you'll need to execute the following:
+
+```
+echo 'export PATH=/LUSTRE/apps/workshop/miniconda3/bin:$PATH' >> ~/.bashrc
+echo 'export PATH=/LUSTRE/apps/workshop/transrate-1.0.3-linux-x86_64:$PATH' >> ~/.bashrc
+source ~/.bashrc
+```
+
+
 
 ## Future Cluster Use
 

diff --git a/docs/sourmash-taxonomic-classification.md b/docs/sourmash-taxonomic-classification.md
@@ -65,6 +65,18 @@ anyway. It can help you quickly locate potential contamination in your sequencin
 wouldn't expect to find mouse RNA in the ocean, but it is a commonly sequenced organism
 and thus if you find it, if may be a contaminant). 
 
+```
+ln -fs /LUSTRE/bioinformatica_data/bioinformatica2018/sourmash_databases/genbank-rna-vertebrate_other-k31.tar.gz .
+ln -fs /LUSTRE/bioinformatica_data/bioinformatica2018/sourmash_databases/genbank-rna-vertebrate_mammalian-k31.tar.gz .
+ln -fs /LUSTRE/bioinformatica_data/bioinformatica2018/sourmash_databases/genbank-rna-invertebrate-k31.tar.gz .
+ln -fs /LUSTRE/bioinformatica_data/bioinformatica2018/sourmash_databases/genbank-rna-fungi-k31.tar.gz .
+ln -fs /LUSTRE/bioinformatica_data/bioinformatica2018/sourmash_databases/genbank-rna-plant-k31.tar.gz .
+ln -fs /LUSTRE/bioinformatica_data/bioinformatica2018/sourmash_databases/genbank-rna-protozoa-k31.tar.gz .
+ln -fs /LUSTRE/bioinformatica_data/bioinformatica2018/sourmash_databases/mmetsp-k31-named.tar.gz .
+```
+
+> Note, if you want to download these files instead, do:
+
 ```
 wget -O genbank-rna-vertebrate_other-k31.tar.gz https://osf.io/qgyax/download
 wget -O genbank-rna-vertebrate_mammalian-k31.tar.gz https://osf.io/6c9uy/download
@@ -74,11 +86,12 @@ wget -O genbank-rna-plant-k31.tar.gz https://osf.io/kctus/download
 wget -O genbank-rna-protozoa-k31.tar.gz https://osf.io/fnu2q/download
 wget -O mmetsp-k31-named.tar.gz https://osf.io/cdvqn/download
 ```
+> but this will not work on the nodes on the cicese cluster!
 
 Next, we need to uncompress the databases:
 
 ```
-for infile in *tar.gz
+for infile in *.tar.gz
 do
     tar xf ${infile}
 done
@@ -157,10 +170,10 @@ python plot-gather.py
 
 this will produce a file 'plot-gather.png' that we need to download in order
 to visualize.
+[Here](https://github.com/ngs-docs/2018-cicese-metatranscriptomics/blob/master/docs/files/plot-gather.png) is a copy of this output
+visualization.
 
 We can see that the reads have more matches than the assembly. 
-[Here](https://github.com/ngs-docs/2018-cicese-metatranscriptomics/blob/master/docs/files/plot-gather.png) is a copy of the output
-visualization.
 
 ## Other notes