Merge branch 'blast_update' into 'master'

Update biodata and blast pages to inlcude BLAST and BLAST_V4 variables

See merge request !195

content/applications/app_specific/bioinformatics_tools/alignment_tools/blast/create_local_blast_database.md

@@ -24,7 +24,7 @@ Simple example of how **makeblastdb** can be run on Crane using SLURM script and
 #SBATCH --output=BlastDB.%J.out
 #SBATCH --error=BlastDB.%J.err
 
-module load blast/2.7
+module load blast/2.10
 
 makeblastdb -in input_reads.fasta -dbtype nucl -out input_reads_db
 {{< /highlight >}}

content/applications/app_specific/bioinformatics_tools/alignment_tools/blast/running_blast_alignment.md

@@ -31,27 +31,18 @@ These BLAST alignment commands are multi-threaded, and therefore using the BLAST
 HCC hosts multiple BLAST databases and indices on Crane. In order to use these resources, the ["biodata" module] ({{<relref "/applications/app_specific/bioinformatics_tools/biodata_module">}}) needs to be loaded first. The **$BLAST** variable contains the following currently available databases:
 
 - **16SMicrobial**
-- **env_nt**
-- **est**
-- **est_human**
-- **est_mouse**
-- **est_others**
-- **gss**
-- **human_genomic**
-- **human_genomic_transcript**
-- **mouse_genomic_transcript**
 - **nr**
 - **nt**
-- **other_genomic**
 - **refseq_genomic**
 - **refseq_rna**
-- **sts**
 - **swissprot**
-- **tsa_nr**
-- **tsa_nt**
 
-If you want to create and use a BLAST database that is not mentioned above, check [Create Local BLAST Database]({{<relref "create_local_blast_database" >}}).
+If you want to create and use a BLAST database that is not mentioned above, check [Create Local BLAST Database]({{<relref "create_local_blast_database" >}}). If you want a database to be added to the ["biodata" module] ({{<relref "/applications/app_specific/bioinformatics_tools/biodata_module">}}), please send a request to bcrf-support@unl.edu.
 
+{{% notice info %}}
+**To access the older format of BLAST databases that work with BLAST+ 2.9 and lower, please use the variable BLAST_V4.**
+**The variable BLAST points to the directory with the new version 5 of the nucleotide and protein databases required for BLAST+ 2.10 and higher.**
+{{% /notice %}}
 
 Basic SLURM example of nucleotide BLAST run against the non-redundant **nt** BLAST database with `8 CPUs` is provided below. When running BLAST alignment, it is recommended to first copy the query and database files to the **/scratch/** directory of the worker node. Moreover, the BLAST output is also saved in this directory (**/scratch/blastn_output.alignments**). After BLAST finishes, the output file is copied from the worker node to your current work directory.
 {{% notice info %}}
@@ -70,7 +61,7 @@ Basic SLURM example of nucleotide BLAST run against the non-redundant **nt** BL
 #SBATCH --output=BlastN.%J.out
 #SBATCH --error=BlastN.%J.err
 
-module load blast/2.7
+module load blast/2.10
 module load biodata/1.0
 
 cd $WORK/<project_folder>
@@ -110,7 +101,7 @@ Basic SLURM example of protein BLAST run against the non-redundant **nr **BLAS
 #SBATCH --output=BlastX.%J.out
 #SBATCH --error=BlastX.%J.err
 
-module load blast/2.7
+module load blast/2.10
 module load biodata/1.0
 
 cd $WORK/<project_folder>

content/applications/app_specific/bioinformatics_tools/biodata_module.md

@@ -23,6 +23,10 @@ The major environment variables are:
 **$INDICES** - Directory containing indices for bowtie, bowtie2, bwa for all available genomes  
 **$UNIPROT** - Directory containing latest release of full UniProt database
 
+{{% notice info %}}
+**To access the older format of BLAST databases that work with BLAST+ 2.9 and lower, please use the variable BLAST_V4.**
+**The variable BLAST points to the directory with the new version 5 of the nucleotide and protein databases required for BLAST+ 2.10 and higher.**
+{{% /notice %}}
 
 In order to check what genomes are available, you can type:
 {{< highlight bash >}}
@@ -69,7 +73,7 @@ An example of BLAST run against the non-redundant nucleotide database available
 #SBATCH --output=BlastN.%J.out
 #SBATCH --error=BlastN.%J.err
 
-module load blast/2.7
+module load blast/2.10
 module load biodata
 cp $BLAST/nt.* /scratch
 cp input_reads.fasta /scratch