Merge branch 'master' of https://git.unl.edu/hcc/hcc-docs into 2013attachments

content/faq/_index.md

@@ -173,5 +173,5 @@ Of course! We have an open door policy and invite you to stop by
 anytime Monday through Friday between 9 am and 5 pm. One of the HCC
 staff would be happy to help you with whatever problem or question you
 have.  Alternatively, you can drop one of us a line and we'll arrange a
-time to meet (http://hcc.unl.edu/contact-us). 
+time to meet:  [Contact Us](https://hcc.unl.edu/contact-us).
 

content/guides/running_applications/bioinformatics_tools/alignment_tools/blast/_index.md

@@ -7,7 +7,7 @@ weight = "52"
 
 [BLAST] (https://blast.ncbi.nlm.nih.gov/Blast.cgi) is a local alignment tool that finds similarity between sequences. This tool compares nucleotide or protein sequences to sequence databases, and calculates significance of matches. Sometimes these input sequences are large and using the command-line BLAST is required.
 
-The following pages, [Create Local BLAST Database](create_local_blast_database) and [Running BLAST Alignment](running_blast_alignment) describe how to run some of the most common BLAST executables as a single job using the SLURM scheduler on HCC.
+The following pages, [Create Local BLAST Database]({{<relref "create_local_blast_database" >}}) and [Running BLAST Alignment]({{<relref "running_blast_alignment" >}}) describe how to run some of the most common BLAST executables as a single job using the SLURM scheduler on HCC.
 
 
 ### Useful Information

content/guides/running_applications/bioinformatics_tools/alignment_tools/blast/running_blast_alignment.md

@@ -28,7 +28,7 @@ $ blastn -help
 These BLAST alignment commands are multi-threaded, and therefore using the BLAST option **-num_threads <number_of_CPUs>** is recommended.
 
 
-HCC hosts multiple BLAST databases and indices on both Tusker and Crane. In order to use these resources, the ["biodata" module] (../../../biodata_module) needs to be loaded first. The **$BLAST** variable contains the following currently available databases:
+HCC hosts multiple BLAST databases and indices on both Tusker and Crane. In order to use these resources, the ["biodata" module] ({{<relref "/guides/running_applications/bioinformatics_tools/biodata_module">}}) needs to be loaded first. The **$BLAST** variable contains the following currently available databases:
 
 - **16SMicrobial**
 - **env_nt**
@@ -50,12 +50,13 @@ HCC hosts multiple BLAST databases and indices on both Tusker and Crane. In orde
 - **tsa_nr**
 - **tsa_nt**
 
-If you want to create and use a BLAST database that is not mentioned above, check [Create Local BLAST Database](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" >}}).
 
 
 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 %}}
 **Please note that the worker nodes can not write to the */home/* directories and therefore you need to run your job from your */work/* directory.**
+**This example will first copy your database to faster local storage called “scratch”.  This can greatly improve performance!**
 {{% /notice %}}
 
 {{% panel header="`blastn_alignment.submit`"%}}
@@ -95,6 +96,7 @@ The default BLAST output is in pairwise format. However, BLAST’s parameter **-
 Basic SLURM example of protein BLAST run against the non-redundant **nr **BLAST database with tabular output format and `8 CPUs` is shown below. Similarly as before, the query and database files are copied to the **/scratch/** directory. The BLAST output is also saved in this directory (**/scratch/blastx_output.alignments**). After BLAST finishes, the output file is copied from the worker node to your current work directory.
 {{% notice info %}}
 **Please note that the worker nodes can not write to the */home/* directories and therefore you need to run your job from your */work/* directory.**
+**This example will first copy your database to faster local storage called “scratch”.  This can greatly improve performance!**
 {{% /notice %}}
 
 {{% panel header="`blastx_alignment.submit`"%}}

content/guides/running_applications/bioinformatics_tools/alignment_tools/bwa/_index.md

@@ -36,4 +36,4 @@ $  bwa COMMAND
 or check the [BWA manual] (http://bio-bwa.sourceforge.net/bwa.shtml).
 
 
-The page[Running BWA Commands](running_bwa_commands) shows how to run BWA on HCC.
+The page [Running BWA Commands]({{<relref "running_bwa_commands" >}}) shows how to run BWA on HCC.

content/guides/running_applications/bioinformatics_tools/alignment_tools/tophat_tophat2.md

@@ -14,7 +14,7 @@ The basic usage of TopHat2 is:
 {{< highlight bash >}}
 $ [tophat|tophat2] [options] index_prefix [input_reads_pair_1.[fasta|fastq] input_reads_pair_2.[fasta|fastq] | input_reads.[fasta|fastq]]
 {{< /highlight >}}
-where **index_prefix** is the basename of the genome index to be searched. This index is generated prior running TopHat/TopHat2 by using [Bowtie](bowtie)/[Bowtie2](bowtie2). 
+where **index_prefix** is the basename of the genome index to be searched. This index is generated prior running TopHat/TopHat2 by using [Bowtie]({{<relref "bowtie" >}})/[Bowtie2]({{<relref "bowtie2" >}}). 
 
 TopHat2 uses single or comma-separated list of paired-end and single-end reads in fasta or fastq format. The single-end reads need to be provided after the paired-end reads.
 

content/guides/running_applications/bioinformatics_tools/biodata_module/_index.md

@@ -80,4 +80,4 @@ cp /scratch/blast_nucleotide.results .
 
 
 The organisms and their appropriate environmental variables for all genomes and chromosome files, as well as for short read aligned indices are shown on the link below:  
-[Organisms](#organisms)
+[Organisms]({{<relref "organisms" >}})

content/guides/running_applications/bioinformatics_tools/data_manipulation_tools/bamtools/_index.md

@@ -36,4 +36,4 @@ $ bamtools help COMMAND
 or check the BamTools web, https://github.com/pezmaster31/bamtools/wiki.
 
 
-The page [Running BamTools Commands](running_bamtools_commands) shows how to run BamTools on HCC.
+The page [Running BamTools Commands]({{<relref "running_bamtools_commands" >}}) shows how to run BamTools on HCC.

content/guides/running_applications/bioinformatics_tools/data_manipulation_tools/samtools/_index.md

@@ -42,4 +42,4 @@ $ samtools COMMAND
 or check the [SAMtools manual] (http://www.htslib.org/doc/samtools.html).
 
 
-The page [Running SAMtools Commands](running_samtools_commands) shows how to run SAMtools on HCC.
+The page [Running SAMtools Commands]({{<relref "running_samtools_commands" >}}) shows how to run SAMtools on HCC.