Commit 7399a2cf authored by John Thiltges's avatar John Thiltges
Browse files

Correct markdown links (removing space) and switch renderer to Hugo default

parent 56817e74
......@@ -42,9 +42,5 @@ weight = 10
# Hugo v0.60+ switched renderer from blackfriday to goldmark
# - Allow unsafe for docdock template rendering
#[markup.goldmark.renderer]
#unsafe = true
# FIXME: Use blackfriday renderer until we update the content to render with goldmark
[markup]
defaultMarkdownHandler = "blackfriday"
[markup.goldmark.renderer]
unsafe = true
......@@ -15,7 +15,7 @@ Materials
Software Carpentry
Lessons: <a href="http://eharstad.github.io/2015-09-08-UNL/" class="external-link">http://eharstad.github.io/2015-09-08-UNL/</a>
[Slides for Day 1] (https://unl.box.com/s/3tz0e3tbxzx9wt8s5l65e1w3fm1w4ojx) (Software Carpentry Introduction)
[Slides for Day 1](https://unl.box.com/s/3tz0e3tbxzx9wt8s5l65e1w3fm1w4ojx) (Software Carpentry Introduction)
[Slides for Day 2](https://unl.box.com/s/8ckxlt7f9geiphiomjodesx9a2nw664b) (Morning Session)
......
......@@ -57,7 +57,7 @@ they were at the time of our last backup. Please note that any changes
made to the files between when the backup was made and when you deleted
them will not be preserved. To have these files restored, please contact
HCC Support at
{{< icon name="envelope" >}}[hcc-support@unl.edu] (mailto:hcc-support@unl.edu)
{{< icon name="envelope" >}}[hcc-support@unl.edu](mailto:hcc-support@unl.edu)
as soon as possible.
**If the files were in your $WORK directory (/work/group/user/):** No.
......@@ -78,7 +78,7 @@ Please stop by
[our offices](http://hcc.unl.edu/location)
along with a photo ID and we will be happy to activate it for you. If
you are not local to Omaha or Lincoln, contact us at
{{< icon name="envelope" >}}[hcc-support@unl.edu] (mailto:hcc-support@unl.edu)
{{< icon name="envelope" >}}[hcc-support@unl.edu](mailto:hcc-support@unl.edu)
and we will help you activate Duo remotely.
**If you have activated Duo previously but now have a different phone
......@@ -90,7 +90,7 @@ Duo and update your account with your new phone number.
**If you have activated Duo previously and have the same phone number:**
Email us at
{{< icon name="envelope" >}}[hcc-support@unl.edu] (mailto:hcc-support@unl.edu)
{{< icon name="envelope" >}}[hcc-support@unl.edu](mailto:hcc-support@unl.edu)
from the email address your account is registered under and we will send
you a new link that you can use to activate Duo.
......@@ -132,7 +132,7 @@ is produced.
**If you are running from inside your $WORK directory:**
Contact us at
{{< icon name="envelope" >}}[hcc-support@unl.edu] (mailto:hcc-support@unl.edu)
{{< icon name="envelope" >}}[hcc-support@unl.edu](mailto:hcc-support@unl.edu)
with your login, the name of the cluster you are running on, and the
full path to your submit script and we will be happy to help solve the
issue.
......@@ -160,7 +160,7 @@ For additional details on how to monitor usage on jobs, check out the
documentation on [Monitoring Jobs]({{< relref "monitoring_jobs" >}}).
If you continue to run into issues, please contact us at
{{< icon name="envelope" >}}[hcc-support@unl.edu] (mailto:hcc-support@unl.edu)
{{< icon name="envelope" >}}[hcc-support@unl.edu](mailto:hcc-support@unl.edu)
for additional assistance.
#### I want to talk to a human about my problem. Can I do that?
......
......@@ -2,6 +2,6 @@
title = "Footer"
+++
{{< icon name="copyright-mark" >}} [Holland Computing Center] (https://hcc.unl.edu) | 118 Schorr Center, Lincoln NE 68588 | {{< icon name="envelope" >}}[hcc-support@unl.edu] (mailto:hcc-support@unl.edu) | {{< icon name="phone-alt" >}}402-472-5041
{{< icon name="copyright-mark" >}} [Holland Computing Center](https://hcc.unl.edu) | 118 Schorr Center, Lincoln NE 68588 | {{< icon name="envelope" >}}[hcc-support@unl.edu](mailto:hcc-support@unl.edu) | {{< icon name="phone-alt" >}}402-472-5041
See something wrong? Help us fix it by [contributing](https://git.unl.edu/hcc/hcc-docs/blob/master/CONTRIBUTING.md)!
......@@ -35,13 +35,13 @@ If you *are not* currently using Duo with your TrueYou account:
Faculty/staff members with a verified NU telephone number can enroll by
phone. If you would like an HCC staff member to call your NU telephone
number to enroll, please email
{{< icon name="envelope" >}}[hcc-support@unl.edu] (mailto:hcc-support@unl.edu)
{{< icon name="envelope" >}}[hcc-support@unl.edu](mailto:hcc-support@unl.edu)
with a time you will be available.
If you *are* currently using Duo with your TrueYou account:
1. You can request to use the same phone for HCC's Duo as you are using for TrueYou.
Please contact [hcc-support@unl.edu] (mailto:hcc-support@unl.edu) with the request
Please contact [hcc-support@unl.edu](mailto:hcc-support@unl.edu) with the request
using the email address associated with your TrueYou account. In the email, include
the last 4 digits of the phone number for verification.
......@@ -72,7 +72,7 @@ exactly as before.
After 10 failed authentication attempts, the user's account is
disabled. If this is the case, then the user needs to send an email to
[hcc-support@unl.edu] (mailto:hcc-support@unl.edu)
[hcc-support@unl.edu](mailto:hcc-support@unl.edu)
including his/her username and the reason why multiple failed
authentication attempts occurred.
{{% /notice %}}
......@@ -92,7 +92,7 @@ Simply tap `Approve` to verify the login.
{{% notice warning%}}**If you receive a verification request you didn't initiate, deny the
request and contact HCC immediately via email at
[hcc-support@unl.edu] (mailto:hcc-support@unl.edu)**
[hcc-support@unl.edu](mailto:hcc-support@unl.edu)**
{{% /notice %}}
In the terminal, the login will now complete and the user will logged in
......
......@@ -173,7 +173,7 @@ precious or irreproducible data should not be placed or left on Anvil**.
subscription is required. As part of HCC's Globus Provider Plan,
HCC can provide this on a per-user basis free of charge. If you are
interested in Globus Plus, please email
{{< icon name="envelope" >}}[hcc-support@unl.edu] (mailto:hcc-support@unl.edu)
{{< icon name="envelope" >}}[hcc-support@unl.edu](mailto:hcc-support@unl.edu)
with your request and a brief explanation.
## Backups
......@@ -192,6 +192,6 @@ disaster recovery backups should not be the only source of backups for
important data. The backup policies are subject to change without prior
notice. To retrieve your backups, please contact HCC. If you have
special concerns please contact us at
{{< icon name="envelope" >}}[hcc-support@unl.edu] (mailto:hcc-support@unl.edu).
{{< icon name="envelope" >}}[hcc-support@unl.edu](mailto:hcc-support@unl.edu).
......@@ -13,5 +13,5 @@ list of available images.
{{< /sorttable >}}
Additional images can be produced by HCC staff by request at
{{< icon name="envelope" >}}[hcc-support@unl.edu] (mailto:hcc-support@unl.edu).
{{< icon name="envelope" >}}[hcc-support@unl.edu](mailto:hcc-support@unl.edu).
 
......@@ -63,4 +63,4 @@ At this point, your instance should have a status of *Active*. Connect
to your instance and ensure that everything works as expected.
{{% notice warning %}}
If your instance ends in an "Error" state or you have any issues or questions with resizing, please contact us at [hcc-support@unl.edu] (mailto:hcc-support@unl.edu) for assistance.{{% /notice %}}
If your instance ends in an "Error" state or you have any issues or questions with resizing, please contact us at [hcc-support@unl.edu](mailto:hcc-support@unl.edu) for assistance.{{% /notice %}}
......@@ -26,6 +26,6 @@ resources, that can be accommodated on a fee basis, depending on the
amount needed.  Please see the HCC
[Priority Access Pricing](http://hcc.unl.edu/priority-access-pricing) page for specific costs.
*By default, no public IP addresses are provided.*
Please contact {{< icon name="envelope" >}}[hcc-support@unl.edu] (mailto:hcc-support@unl.edu)
Please contact {{< icon name="envelope" >}}[hcc-support@unl.edu](mailto:hcc-support@unl.edu)
for more details.
......@@ -4,10 +4,10 @@ description = "How to access and use a Jupyter Notebook"
weight = 20
+++
- [Connecting to JupyterHub] (#connecting-to-jupyterhub)
- [Running Code] (#running-code)
- [Opening a Terminal] (#opening-a-terminal)
- [Using Custom Packages] (#using-custom-packages)
- [Connecting to JupyterHub](#connecting-to-jupyterhub)
- [Running Code](#running-code)
- [Opening a Terminal](#opening-a-terminal)
- [Using Custom Packages](#using-custom-packages)
## Connecting to JupyterHub
-----------------------
......@@ -42,7 +42,7 @@ Select the other options based on your computing needs. Note that a SLURM Job wi
1. From your user home page, select "terminal" from the "New" drop-down menu.
{{< figure src="/images/jupyterTerminal.png">}}
2. A terminal opens in a new tab. You can enter [Linux commands] ({{< relref "basic_linux_commands" >}})
2. A terminal opens in a new tab. You can enter [Linux commands]({{< relref "basic_linux_commands" >}})
at the prompt.
{{< figure src="/images/jupyterTerminal2.png">}}
......
......@@ -46,7 +46,7 @@ The basic usage of ``perf-report` is:
{{< highlight bash >}}
perf-report [OPTION...] PROGRAM [PROGRAM_ARGS]
or
perf-report [OPTION...] (mpirun|mpiexec|aprun|...) [MPI_ARGS] PROGRAM [PROGRAM_ARGS]
perf-report [OPTION...](mpirun|mpiexec|aprun|...) [MPI_ARGS] PROGRAM [PROGRAM_ARGS]
{{< /highlight >}}
{{% /panel %}}
......
......@@ -5,7 +5,7 @@ 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.
[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]({{<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.
......
......@@ -20,7 +20,7 @@ $ blastn -query input_reads.fasta -db input_reads_db -out blastn_output.alignmen
{{< /highlight >}}
where **input_reads.fasta** is an input file of sequence data in fasta format, **input_reads_db** is the generated BLAST database, and **blastn_output.alignments** is the output file where the alignments are stored.
Additional parameters can be found in the [BLAST manual] (https://www.ncbi.nlm.nih.gov/books/NBK279690/), or by typing:
Additional parameters can be found in the [BLAST manual](https://www.ncbi.nlm.nih.gov/books/NBK279690/), or by typing:
{{< highlight bash >}}
$ blastn -help
{{< /highlight >}}
......@@ -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 Crane. In order to use these resources, the ["biodata" module] ({{<relref "/applications/app_specific/bioinformatics_tools/biodata_module">}}) needs to be loaded first. The **$BLAST** variable contains the following currently available databases:
HCC hosts multiple BLAST databases and indices on Crane. In order to use these resources, the ["biodata" module]({{<relref "/applications/app_specific/bioinformatics_tools/biodata_module">}}) needs to be loaded first. The **$BLAST** variable contains the following currently available databases:
- **16SMicrobial**
- **nr**
......@@ -37,7 +37,7 @@ HCC hosts multiple BLAST databases and indices on Crane. In order to use these r
- **refseq_rna**
- **swissprot**
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.
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.**
......@@ -81,7 +81,7 @@ $ blastn -query input_reads.fasta -db input_reads_db -out blastn_output.alignmen
{{< /highlight >}}
The default BLAST output is in pairwise format. However, BLAST’s parameter **-outfmt** supports output in [different formats] (https://www.ncbi.nlm.nih.gov/books/NBK279684/) that are easier for parsing.
The default BLAST output is in pairwise format. However, BLAST’s parameter **-outfmt** supports output in [different formats](https://www.ncbi.nlm.nih.gov/books/NBK279684/) that are easier for parsing.
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.
......
......@@ -15,7 +15,7 @@ $ blat database query output_alignment.txt [options]
where **database** is the name of the database used for the alignment, **query** is the name of the input file of sequence data in `fasta/nib/2bit` format, and **output_alignment.txt** is the output alignment file.
Additional parameters for BLAT alignment can be found in the [manual] (http://genome.ucsc.edu/FAQ/FAQblat), or by using:
Additional parameters for BLAT alignment can be found in the [manual](http://genome.ucsc.edu/FAQ/FAQblat), or by using:
{{< highlight bash >}}
$ blat
{{< /highlight >}}
......
......@@ -5,7 +5,7 @@ weight = "10"
+++
[Bowtie] (http://bowtie-bio.sourceforge.net/index.shtml) is an ultrafast and memory-efficient aligner for large sets of sequencing reads to a reference genome. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small. Bowtie also supports usage of multiple processors to achieve greater alignment speed.
[Bowtie](http://bowtie-bio.sourceforge.net/index.shtml) is an ultrafast and memory-efficient aligner for large sets of sequencing reads to a reference genome. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small. Bowtie also supports usage of multiple processors to achieve greater alignment speed.
The first and basic step of running Bowtie is to build and format an index from the reference genome. The basic usage of this command, **bowtie-build** is:
......@@ -19,7 +19,7 @@ After the index of the reference genome is generated, the next step is to align
$ bowtie [-q|-f|-r|-c] index_prefix [-1 input_reads_pair_1.[fasta|fastq] -2 input_reads_pair_2.[fasta|fastq] | input_reads.[fasta|fastq]] [options]
{{< /highlight >}}
where **index_prefix** is the generated index using the **bowtie-build** command, and **options** are optional parameters that can be found in the [Bowtie
manual] (http://bowtie-bio.sourceforge.net/manual.shtml).
manual](http://bowtie-bio.sourceforge.net/manual.shtml).
Bowtie supports both single-end (`input_reads.[fasta|fastq]`) and paired-end (`input_reads_pair_1.[fasta|fastq]`, `input_reads_pair_2.[fasta|fastq]`) files in fasta or fastq format. The format of the input files also needs to be specified by using the following flags: **-q** (fastq files), **-f** (fasta files), **-r** (raw one-sequence per line), or **-c** (sequences given on command line).
......
......@@ -5,7 +5,7 @@ weight = "10"
+++
[Bowtie2] (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml) is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. Although Bowtie and Bowtie2 are both fast read aligners, there are few main differences between them:
[Bowtie2](http://bowtie-bio.sourceforge.net/bowtie2/index.shtml) is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. Although Bowtie and Bowtie2 are both fast read aligners, there are few main differences between them:
- Bowtie2 supports gapped alignment with affine gap penalties, without restrictions on the number of gaps and gap lengths.
- Bowtie supports reads longer than 50bp and is generally faster, more sensitive, and uses less memory than Bowtie.
......@@ -28,7 +28,7 @@ The command **bowtie2** takes a Bowtie2 index and set of sequencing read files a
{{< highlight bash >}}
$ bowtie2 -x index_prefix [-q|--qseq|-f|-r|-c] [-1 input_reads_pair_1.[fasta|fastq] -2 input_reads_pair_2.[fasta|fastq] | -U input_reads.[fasta|fastq]] -S bowtie2_alignments.sam [options]
{{< /highlight >}}
where **index_prefix** is the generated index using the **bowtie2-build** command, and **options** are optional parameters that can be found in the [Bowtie2 manual] (http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml). Bowtie2 supports both single-end (`input_reads.[fasta|fastq]`) and paired-end (`input_reads_pair_1.[fasta|fastq]`, `input_reads_pair_2.[fasta|fastq]`) files in fasta or fastq format. The format of the input files also needs to be specified by using one of the following flags: **-q** (fastq files), **--qseq** (Illumina's qseq format), **-f** (fasta files), **-r** (raw one sequence per line), or **-c** (sequences given on command line).
where **index_prefix** is the generated index using the **bowtie2-build** command, and **options** are optional parameters that can be found in the [Bowtie2 manual](http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml). Bowtie2 supports both single-end (`input_reads.[fasta|fastq]`) and paired-end (`input_reads_pair_1.[fasta|fastq]`, `input_reads_pair_2.[fasta|fastq]`) files in fasta or fastq format. The format of the input files also needs to be specified by using one of the following flags: **-q** (fastq files), **--qseq** (Illumina's qseq format), **-f** (fasta files), **-r** (raw one sequence per line), or **-c** (sequences given on command line).
An example of how to run Bowtie2 local alignment on Crane with paired-end fasta files and `8 CPUs` is shown below:
......
......@@ -33,7 +33,7 @@ For detailed description and more information on a specific command, just type:
{{< highlight bash >}}
$ bwa COMMAND
{{< /highlight >}}
or check the [BWA manual] (http://bio-bwa.sourceforge.net/bwa.shtml).
or check the [BWA manual](http://bio-bwa.sourceforge.net/bwa.shtml).
The page [Running BWA Commands]({{<relref "running_bwa_commands" >}}) shows how to run BWA on HCC.
......@@ -5,7 +5,7 @@ weight = "10"
+++
[Clustal Omega] (http://www.clustal.org/omega/) is a general purpose multiple sequence alignment (MSA) tool used mainly with protein, as well as DNA and RNA sequences. Clustal Omega is fast and scalable aligner that can align datasets of hundreds of thousands of sequences in reasonable time.
[Clustal Omega](http://www.clustal.org/omega/) is a general purpose multiple sequence alignment (MSA) tool used mainly with protein, as well as DNA and RNA sequences. Clustal Omega is fast and scalable aligner that can align datasets of hundreds of thousands of sequences in reasonable time.
The general usage of Clustal Omega is:
......
......@@ -5,7 +5,7 @@ weight = "10"
+++
[TopHat] (https://ccb.jhu.edu/software/tophat/index.shtml) is a fast splice junction mapper for RNA-Seq data. It first aligns RNA-Seq reads to reference genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons.
[TopHat](https://ccb.jhu.edu/software/tophat/index.shtml) is a fast splice junction mapper for RNA-Seq data. It first aligns RNA-Seq reads to reference genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons.
Although there is no difference between the available options for both TopHat and TopHat2 and the number of output files, TopHat2 incorporates many significant improvements to TopHat. The TopHat package at HCC supports both **tophat** and **tophat2**.
......@@ -19,7 +19,7 @@ where **index_prefix** is the basename of the genome index to be searched. This
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.
More advanced TopHat2 options can be found in [its manual] (https://ccb.jhu.edu/software/tophat/manual.shtml), or by typing:
More advanced TopHat2 options can be found in [its manual](https://ccb.jhu.edu/software/tophat/manual.shtml), or by typing:
{{< highlight bash >}}
$ tophat2 -h
{{< /highlight >}}
......
......@@ -5,7 +5,7 @@ weight = "52"
+++
The SAM format is a standard format for storing large nucleotide sequence alignments. The BAM format is just the binary form from SAM. [SAMtools] (http://www.htslib.org/) is a toolkit for manipulating alignments in SAM/BAM format, including sorting, merging, indexing and generating alignments in a per-position format.
The SAM format is a standard format for storing large nucleotide sequence alignments. The BAM format is just the binary form from SAM. [SAMtools](http://www.htslib.org/) is a toolkit for manipulating alignments in SAM/BAM format, including sorting, merging, indexing and generating alignments in a per-position format.
The basic usage of SAMtools is:
......@@ -39,7 +39,7 @@ For detailed description and more information on a specific command, just type:
{{< highlight bash >}}
$ samtools COMMAND
{{< /highlight >}}
or check the [SAMtools manual] (http://www.htslib.org/doc/samtools.html).
or check the [SAMtools manual](http://www.htslib.org/doc/samtools.html).
The page [Running SAMtools Commands]({{<relref "running_samtools_commands" >}}) shows how to run SAMtools on HCC.
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