From f803ba9636f5cbbe9b097887a12bf4fabf2499de Mon Sep 17 00:00:00 2001
From: Adam Caprez <acaprez2@unl.edu>
Date: Fri, 19 Apr 2019 18:02:56 +0000
Subject: [PATCH] Add relref to links under bioinformatics_tools.
---
.../bioinformatics_tools/alignment_tools/blast/_index.md | 2 +-
.../alignment_tools/blast/running_blast_alignment.md | 4 ++--
.../bioinformatics_tools/alignment_tools/bwa/_index.md | 2 +-
.../bioinformatics_tools/alignment_tools/tophat_tophat2.md | 2 +-
.../bioinformatics_tools/biodata_module/_index.md | 2 +-
.../data_manipulation_tools/bamtools/_index.md | 2 +-
.../data_manipulation_tools/samtools/_index.md | 2 +-
7 files changed, 8 insertions(+), 8 deletions(-)
diff --git a/content/guides/running_applications/bioinformatics_tools/alignment_tools/blast/_index.md b/content/guides/running_applications/bioinformatics_tools/alignment_tools/blast/_index.md
index a709aaef..deb9548c 100644
--- a/content/guides/running_applications/bioinformatics_tools/alignment_tools/blast/_index.md
+++ b/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
diff --git a/content/guides/running_applications/bioinformatics_tools/alignment_tools/blast/running_blast_alignment.md b/content/guides/running_applications/bioinformatics_tools/alignment_tools/blast/running_blast_alignment.md
index a3b03c7a..babb6493 100644
--- a/content/guides/running_applications/bioinformatics_tools/alignment_tools/blast/running_blast_alignment.md
+++ b/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**
@@ -50,7 +50,7 @@ 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.
diff --git a/content/guides/running_applications/bioinformatics_tools/alignment_tools/bwa/_index.md b/content/guides/running_applications/bioinformatics_tools/alignment_tools/bwa/_index.md
index 5d1e3510..5b770061 100644
--- a/content/guides/running_applications/bioinformatics_tools/alignment_tools/bwa/_index.md
+++ b/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.
diff --git a/content/guides/running_applications/bioinformatics_tools/alignment_tools/tophat_tophat2.md b/content/guides/running_applications/bioinformatics_tools/alignment_tools/tophat_tophat2.md
index 92a3208a..69ac4d03 100644
--- a/content/guides/running_applications/bioinformatics_tools/alignment_tools/tophat_tophat2.md
+++ b/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.
diff --git a/content/guides/running_applications/bioinformatics_tools/biodata_module/_index.md b/content/guides/running_applications/bioinformatics_tools/biodata_module/_index.md
index 7fd7db27..45f9d16e 100644
--- a/content/guides/running_applications/bioinformatics_tools/biodata_module/_index.md
+++ b/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" >}})
diff --git a/content/guides/running_applications/bioinformatics_tools/data_manipulation_tools/bamtools/_index.md b/content/guides/running_applications/bioinformatics_tools/data_manipulation_tools/bamtools/_index.md
index 9399d8e3..efe441b2 100644
--- a/content/guides/running_applications/bioinformatics_tools/data_manipulation_tools/bamtools/_index.md
+++ b/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.
diff --git a/content/guides/running_applications/bioinformatics_tools/data_manipulation_tools/samtools/_index.md b/content/guides/running_applications/bioinformatics_tools/data_manipulation_tools/samtools/_index.md
index 0246ba99..df9a00e2 100644
--- a/content/guides/running_applications/bioinformatics_tools/data_manipulation_tools/samtools/_index.md
+++ b/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.
--
GitLab