Differences

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--- diamond-software [2018/11/04 16:06] – aorth
+++ diamond-software [2022/03/17 09:10] (current) – aorth
@@ Line 5: / Line 5: @@
 ===== Information =====
-  * Version: 0.9.9
+  * Version: 2.0.14
   * Added: November, 2016
-  * Updated: July, 2017
+  * Updated: March, 2022
-  * Link: http://ab.inf.uni-tuebingen.de/software/diamond/
+  * Link: https://github.com/bbuchfink/diamond
 ===== Usage =====
-See which versions of diamond are available:
+See which versions are available:
 <code>$ module avail diamond</code>
-Load the diamond environment module and run it:
+Load one version into your environment and run it:
-<code>$ module load diamond/0.9.9
+<code>$ module load diamond/2.0.14
 $ diamond</code>
@@ Line 46: / Line 46: @@
 <code>$ cd /tmp
-$ wget https://github.com/bbuchfink/diamond/releases/download/v0.9.9/diamond-linux64.tar.gz
+$ wget http://github.com/bbuchfink/diamond/releases/download/v2.0.14/diamond-linux64.tar.gz
+$ sudo mkdir -p /export/apps/diamond/2.0.14/bin
 $ tar xf diamond-linux64.tar.gz
-$ sudo cp diamond diamond_manual.pdf /export/apps/diamond/0.9.9</code>
+$ sudo cp diamond /export/apps/diamond/2.0.14/bin</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
+$ wget ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/prot.accession2taxid.FULL.gz
+$ wget ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdmp.zip
+$ unzip taxdmp.zip
+$ diamond makedb --in nr.gz --db nr --taxonmap prot.accession2taxid.FULL.gz --taxonnodes nodes.dmp --taxonnames names.dmp
 $ sudo mkdir -p /export/data/bio/diamond
 $ sudo cp nr.dmnd /export/data/bio/diamond</code>