From 3ed86938365ce6162dbff62ca5bb9624c53b332b Mon Sep 17 00:00:00 2001
From: Natasha Pavlovikj <npavlovikj2@unl.edu>
Date: Tue, 7 Apr 2020 16:18:24 -0500
Subject: [PATCH] Update biodata and blast pages to inlcude BLAST and BLAST_V4
variables
---
.../blast/create_local_blast_database.md | 2 +-
.../blast/running_blast_alignment.md | 23 ++++++-------------
.../bioinformatics_tools/biodata_module.md | 6 ++++-
3 files changed, 13 insertions(+), 18 deletions(-)
diff --git a/content/applications/app_specific/bioinformatics_tools/alignment_tools/blast/create_local_blast_database.md b/content/applications/app_specific/bioinformatics_tools/alignment_tools/blast/create_local_blast_database.md
index 33f16752..4caf0d48 100644
--- a/content/applications/app_specific/bioinformatics_tools/alignment_tools/blast/create_local_blast_database.md
+++ b/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 >}}
diff --git a/content/applications/app_specific/bioinformatics_tools/alignment_tools/blast/running_blast_alignment.md b/content/applications/app_specific/bioinformatics_tools/alignment_tools/blast/running_blast_alignment.md
index b93fb6d8..936c2ebb 100644
--- a/content/applications/app_specific/bioinformatics_tools/alignment_tools/blast/running_blast_alignment.md
+++ b/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 $WORK/<project_folder>
diff --git a/content/applications/app_specific/bioinformatics_tools/biodata_module.md b/content/applications/app_specific/bioinformatics_tools/biodata_module.md
index 0257bcf5..d7ed97a3 100644
--- a/content/applications/app_specific/bioinformatics_tools/biodata_module.md
+++ b/content/applications/app_specific/bioinformatics_tools/biodata_module.md
@@ -23,6 +23,10 @@ The major environment variables are:
**$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
--
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