Differences

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--- diamond-software [2016/11/23 13:12] – created joguya
+++ diamond-software [2017/07/23 11:25] – aorth
@@ Line 5: / Line 5: @@
 ===== Information =====
-  * Latest Version: 0.8.27
+  * Latest Version: 0.9.9
   * Added: November, 2016
+  * Updated: July, 2017
   * Link: http://ab.inf.uni-tuebingen.de/software/diamond/
@@ Line 12: / Line 13: @@
 See which versions of diamond are available:
-<code>$ module avail diamond
+<code>$ module avail diamond</code>
-</code>
-Load diamond
+Load the diamond environment module and run it:
-<code>$ module load diamond/0.8.27</code>
+<code>$ module load diamond/0.9.9
+$ diamond</code>
 ===== Installation ======
-Notes from the sysadmin during installation:<code>
+Notes from the sysadmin during installation:
-$ cd /tmp/
-$ wget https://github.com/bbuchfink/diamond/releases/download/v0.8.27/diamond-linux64.tar.gz
+<code>$ cd /tmp
-$ tar -xvf diamond-linux64.tar.gz
+$ wget https://github.com/bbuchfink/diamond/releases/download/v0.9.9/diamond-linux64.tar.gz
-$ sudo mkdir -p /export/apps/diamond/0.8.27/
+$ tar xf diamond-linux64.tar.gz
-$ sudo cp diamond diamond_manual.pdf /export/apps/diamond/0.8.27/
+$ sudo cp diamond diamond_manual.pdf /export/apps/diamond/0.9.9</code>
-</code>
+Diamond requires specially formatted databases, which you create using the ''diamond makedb'' subcommand. The input must be a FASTA file, but can be gzip compressed, for example the NR database from NCBI:
+<code>$ wget ftp://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/nr.gz
+$ diamond makedb --in nr.gz -d nr
+$ sudo mkdir -p /export/data/bio/diamond
+$ sudo cp nr.dmnd /export/data/bio/diamond</code>