Merge branch '24-Remove-Tucker' into 'master'

Removed Tucker

Closes #24

See merge request !172

content/Events/2013/supercomputing_mini_workshop_february_27_2013.md

@@ -22,7 +22,7 @@ state-of-the-art supercomputing resources.
 **Logging In**
 
 ``` syntaxhighlighter-pre
-ssh tusker.unl.edu -l demoXXXX
+ssh crane.unl.edu -l demoXXXX
 ```
 
 **[Cypwin Link](http://cygwin.com/install.html)**
@@ -49,7 +49,7 @@ two folders, `serial\_f90` and `parallel\_f90`, in this folder
 
 ``` syntaxhighlighter-pre
 $ ls
-$ scp -r ./demo_code <username>@tusker.unl.edu:/work/demo/<username>
+$ scp -r ./demo_code <username>@crane.unl.edu:/work/demo/<username>
 <enter password>
 ```
 
@@ -59,7 +59,7 @@ Serial Job
 First, you need to login to the cluster
 
 ``` syntaxhighlighter-pre
-$ ssh <username>@tusker.unl.edu
+$ ssh <username>@crane.unl.edu
 <enter password>
 ```
 
@@ -133,14 +133,14 @@ code.  It uses MPI for communication between the parallel processes.
 $ mpif90 fortran_mpi.f90 -o fortran_mpi.x
 ```
 
-Next, we will submit the MPI application to the Tusker cluster scheduler
+Next, we will submit the MPI application to the cluster scheduler
 using the file `submit_tusker.mpi`.
 
 ``` syntaxhighlighter-pre
 $ qsub submit_tusker.mpi
 ```
 
-The Tusker cluster scheduler will pick machines (possibly several,
+The cluster scheduler will pick machines (possibly several,
 depending on availability) to run the parallel MPI application.  You can
 check the status of the job the same way you did with the Serial job:
 

content/applications/app_specific/allinea_profiling_and_debugging/allinea_performance_reports/ray_with_allinea_performance_reports.md

@@ -4,7 +4,7 @@ description = "Example of how to profile Ray using Allinea Performance Reports"
 +++
 
 Simple example of using [Ray]({{< relref "/applications/app_specific/bioinformatics_tools/de_novo_assembly_tools/ray" >}})
-with Allinea PerformanceReports (`perf-report`) on Tusker is shown below:
+with Allinea PerformanceReports (`perf-report`) is shown below:
 
 {{% panel theme="info" header="ray_perf_report.submit" %}}
 {{< highlight batch >}}

content/applications/app_specific/bioinformatics_tools/alignment_tools/clustal_omega.md

@@ -64,5 +64,5 @@ The basic Clustal Omega output produces one alignment file in the specified outp
 
 ### Useful Information
 
-In order to test the Clustal Omega performance on Tusker, we used three DNA and protein input fasta files, `data_1.fasta`, `data_2.fasta`, `data_3.fasta`. Some statistics about the input files and the time and memory resources used by Clustal Omega on Tusker are shown on the table below:
+In order to test the Clustal Omega performance, we used three DNA and protein input fasta files, `data_1.fasta`, `data_2.fasta`, `data_3.fasta`. Some statistics about the input files and the time and memory resources used by Clustal Omega are shown on the table below:
 {{< readfile file="/static/html/clustal_omega.html" >}}

content/applications/app_specific/bioinformatics_tools/de_novo_assembly_tools/oases.md

@@ -59,5 +59,5 @@ Oases produces two additional output files: `transcripts.fa` and `contig-orderin
 
 ### Useful Information
 
-In order to test the Oases (oases/0.2.8) performance on Tusker, we used three paired-end input fastq files, `small_1.fastq` and `small_2.fastq`, `medium_1.fastq` and `medium_2.fastq`, and `large_1.fastq` and `large_2.fastq`. Some statistics about the input files and the time and memory resources used by Oases on Tusker are shown in the table below:
+In order to test the Oases (oases/0.2.8) performance, we used three paired-end input fastq files, `small_1.fastq` and `small_2.fastq`, `medium_1.fastq` and `medium_2.fastq`, and `large_1.fastq` and `large_2.fastq`. Some statistics about the input files and the time and memory resources used by Oases are shown in the table below:
 {{< readfile file="/static/html/oases.html" >}}

content/applications/app_specific/bioinformatics_tools/de_novo_assembly_tools/ray.md

@@ -38,7 +38,7 @@ Ray supports both paired-end (`-p`) and single-end reads (`-s`). Moreover, Ray c
 Ray supports odd values for k-mer equal to or greater than 21 (`-k <kmer_value>`). Ray supports multiple file formats such as `fasta`, `fa`, `fasta.gz`, `fa.gz, `fasta.bz2`, `fa.bz2`, `fastq`, `fq`, `fastq.gz`, `fq.gz`, `fastq.bz2`, `fq.bz2`, `sff`, `csfasta`, `csfa`.
 
 
-Simple SLURM script for running Ray on Tusker with both paired-end and single-end data with `k-mer=31`, `8 CPUs` and `4 GB RAM per CPU` is shown below:
+Simple SLURM script for running Ray with both paired-end and single-end data with `k-mer=31`, `8 CPUs` and `4 GB RAM per CPU` is shown below:
 {{% panel header="`ray.submit`"%}}
 {{< highlight bash >}}
 #!/bin/sh
@@ -76,5 +76,5 @@ One of the most important results are:
 
 ### Useful Information
 
-In order to test the Ray performance on Tusker, we used three paired-end input fastq files, `small_1.fastq` and `small_2.fastq`, `medium_1.fastq` and `medium_2.fastq`, and `large_1.fastq` and `large_2.fastq`. Some statistics about the input files and the time and memory resources used by Ray on Tusker are shown in the table below:
+In order to test the Ray performance, we used three paired-end input fastq files, `small_1.fastq` and `small_2.fastq`, `medium_1.fastq` and `medium_2.fastq`, and `large_1.fastq` and `large_2.fastq`. Some statistics about the input files and the time and memory resources used by Ray are shown in the table below:
 {{< readfile file="/static/html/ray.html" >}}

content/applications/app_specific/bioinformatics_tools/de_novo_assembly_tools/soapdenovo2.md

@@ -94,7 +94,7 @@ q=input_reads.fq
 After creating the configuration file **configFile**, the next step is to run the assembler using this file.
 
 
-Simple SLURM script for running SOAPdenovo2 with `k-mer=31`, `8 CPUSs` and `50GB of RAM` on Tusker is shown below:
+Simple SLURM script for running SOAPdenovo2 with `k-mer=31`, `8 CPUSs` and `50GB of RAM` is shown below:
 {{% panel header="`soapdenovo2.submit`"%}}
 {{< highlight bash >}}
 #!/bin/sh
@@ -128,7 +128,7 @@ output31.contig         output31.edge.gz           output31.links     output31.p
 
 ### Useful Information
 
-In order to test the SOAPdenovo2 (soapdenovo2/r240) performance on Tusker, we used three different size input files. Some statistics about the input files and the time and memory resources used by SOAPdenovo2 are shown in the table below:
+In order to test the SOAPdenovo2 (soapdenovo2/r240) performance, we used three different size input files. Some statistics about the input files and the time and memory resources used by SOAPdenovo2 are shown in the table below:
 {{< readfile file="/static/html/soapdenovo2.html" >}}
 
 In general, SOAPdenovo2 is a memory intensive assembler that requires approximately 30-60 GB memory for assembling 50 million reads. However, SOAPdenovo2 is a fast assembler and it takes around an hour to assemble 50 million reads.

content/applications/app_specific/bioinformatics_tools/de_novo_assembly_tools/trinity/_index.md

@@ -52,7 +52,7 @@ Each step may be run as its own job, providing a workaround for the single job w
 
 ### Useful Information
 
-In order to test the Trinity (trinity/r2014-04-13p1) performance on Tusker, we used three paired-end input fastq files, `small_1.fastq` and `small_2.fastq`, `medium_1.fastq` and `medium_2.fastq`, and `large_1.fastq` and `large_2.fastq`. Some statistics about the input files and the time and memory resources used by Trinity on Tusker are shown in the table below:
+In order to test the Trinity (trinity/r2014-04-13p1) performance, we used three paired-end input fastq files, `small_1.fastq` and `small_2.fastq`, `medium_1.fastq` and `medium_2.fastq`, and `large_1.fastq` and `large_2.fastq`. Some statistics about the input files and the time and memory resources used by Trinity are shown in the table below:
 {{< readfile file="/static/html/trinity.html" >}}
 
 

content/applications/app_specific/bioinformatics_tools/de_novo_assembly_tools/velvet/_index.md

@@ -18,5 +18,5 @@ Each step of Velvet (**velveth** and **velvetg**) may be run as its own job. The
 
 ### Useful Information
 
-In order to test the Velvet (velvet/1.2) performance on Tusker, we used three paired-end input fastq files, `small_1.fastq` and `small_2.fastq`, `medium_1.fastq` and `medium_2.fastq`, and `large_1.fastq` and `large_2.fastq`. Some statistics about the input files and the time and memory resources used by Velvet on Tusker are shown in the table below:
+In order to test the Velvet (velvet/1.2) performance, we used three paired-end input fastq files, `small_1.fastq` and `small_2.fastq`, `medium_1.fastq` and `medium_2.fastq`, and `large_1.fastq` and `large_2.fastq`. Some statistics about the input files and the time and memory resources used by Velvet are shown in the table below:
 {{< readfile file="/static/html/velvet.html" >}}

content/applications/app_specific/bioinformatics_tools/pre_processing_tools/scythe.md

@@ -22,7 +22,7 @@ $ scythe --help
 {{< /highlight >}}
 
 
-Simple Scythe script that uses the `illumina_adapters.fa` file and `input_reads.fastq` for Tusker is shown below:
+Simple Scythe script that uses the `illumina_adapters.fa` file and `input_reads.fastq` is shown below:
 {{% panel header="`scythe.submit`"%}}
 {{< highlight bash >}}
 #!/bin/sh
@@ -52,5 +52,5 @@ Scythe returns fastq file of reads with removed adapter sequences.
 
 ### Useful Information
 
-In order to test the Scythe (scythe/0.991) performance on Tusker, we used three paired-end input fastq files, `small_1.fastq` and `small_2.fastq`, `medium_1.fastq` and `medium_2.fastq`, and `large_1.fastq` and `large_2.fastq`. Some statistics about the input files and the time and memory resources used by Scythe on Tusker are shown in the table below:
+In order to test the Scythe (scythe/0.991) performance , we used three paired-end input fastq files, `small_1.fastq` and `small_2.fastq`, `medium_1.fastq` and `medium_2.fastq`, and `large_1.fastq` and `large_2.fastq`. Some statistics about the input files and the time and memory resources used by Scythe are shown in the table below:
 {{< readfile file="/static/html/scythe.html" >}}

content/applications/app_specific/bioinformatics_tools/pre_processing_tools/sickle.md

@@ -79,5 +79,5 @@ Sickle returns fastq file of reads with trimmed low quality bases from both 3' a
 
 ### Useful Information
 
-In order to test the Sickle (sickle/1.210) performance on Tusker, we used three paired-end input fastq files, `small_1.fastq` and `small_2.fastq`, `medium_1.fastq` and `medium_2.fastq`, and `large_1.fastq` and `large_2.fastq`. Some statistics about the input files and the time and memory resources used by Sickle on Tusker are shown in the table below:
+In order to test the Sickle (sickle/1.210) performance, we used three paired-end input fastq files, `small_1.fastq` and `small_2.fastq`, `medium_1.fastq` and `medium_2.fastq`, and `large_1.fastq` and `large_2.fastq`. Some statistics about the input files and the time and memory resources used by Sickle are shown in the table below:
 {{< readfile file="/static/html/sickle.html" >}}

content/applications/app_specific/running_ocean_land_atmosphere_model_olam.md

@@ -3,7 +3,7 @@ title = "Running OLAM at HCC"
 description = "How to run the OLAM (Ocean Land Atmosphere Model) on HCC resources."
 +++
 
-### OLAM compilation on Tusker
+### OLAM compilation
 ##### pgi/11 compilation with mpi and openmp enabled
 
 1.  Load modules:

content/connecting/for_windows_users.md

@@ -30,16 +30,16 @@ Users]({{< relref "/connecting/for_maclinux_users" >}}).
 --------------
 For Windows 10 users, use the Command Prompt, accessed by entering `cmd` in the start menu, to access to the
 HCC supercomputers. In the Command Prompt,
-type `ssh <username>@tusker.unl.edu` and the corresponding password
-to get access to the HCC cluster **Tusker**. Note that &lt;username&gt;
+type `ssh <username>@crane.unl.edu` and the corresponding password
+to get access to the HCC cluster **Crane**. Note that &lt;username&gt;
 should be replaced by your HCC account username. If you do not have a
 HCC account, please contact a HCC specialist
 ({{< icon name="envelope" >}}[hcc-support@unl.edu] (mailto:hcc-support@unl.edu))
 or go to http://hcc.unl.edu/newusers.
-To use the **Crane** cluster, replace tusker.unl.edu with crane.unl.edu.
+To use the **Rhino** cluster, replace crane.unl.edu with rhino.unl.edu.
 
 {{< highlight bash >}}
-C:\> ssh <username>@tusker.unl.edu
+C:\> ssh <username>@crane.unl.edu
 C:\> <password>
 {{< /highlight >}}
 
@@ -55,10 +55,10 @@ PuTTY: https://www.chiark.greenend.org.uk/~sgtatham/putty/latest.html
 or [Direct Link](https://the.earth.li/~sgtatham/putty/latest/w32/putty.exe)
 
 
-Here we use the HCC cluster **Tusker** for demonstration. To use the
-**Crane** or cluster, replace `tusker.unl.edu` with `crane.unl.edu`.
+Here we use the HCC cluster **Crane** for demonstration. To use the
+**Rhino** or cluster, replace `crane.unl.edu` with `rhino.unl.edu`.
 
-1.  On the first screen, type `tusker.unl.edu` for Host Name, then click
+1.  On the first screen, type `crane.unl.edu` for Host Name, then click
     **Open**. 
     {{< figure src="/images/3178523.png" height="450" >}}
 2.  On the second screen, click on **Yes**.  
@@ -118,28 +118,28 @@ For best results when transfering data to and from the clusters, refer to [Handl
 
 For Windows users, file transferring between your personal computer
 and the HCC supercomputers can be achieved through the command `scp`.
-Here we use **Tusker** for example. **The following commands should be
+Here we use **Crane** for example. **The following commands should be
 executed from your computer. **
 
 **Uploading from local to remote**
 
 {{< highlight bash >}}
-C:\> scp -r .\<folder name> <username>@tusker.unl.edu:/work/<group name>/<username>
+C:\> scp -r .\<folder name> <username>@crane.unl.edu:/work/<group name>/<username>
 {{< /highlight >}}
 
 The above command line transfers a folder from the current directory
 (`.\`) of the your computer to the `$WORK` directory of the HCC
-supercomputer, Tusker. Note that you need to replace `<group name>`
+supercomputer, Crane. Note that you need to replace `<group name>`
 and `<username>` with your HCC group name and username. 
 
 **Downloading from remote to local**
 
 {{< highlight bash >}}
-C:\> scp -r <username>@tusker.unl.edu:/work/<group name>/<username>/<folder name> .\
+C:\> scp -r <username>@crane.unl.edu:/work/<group name>/<username>/<folder name> .\
 {{< /highlight >}}
 
 The above command line transfers a folder from the `$WORK` directory of
-the HCC supercomputer, Tusker, to the current directory (`.\`) of the
+the HCC supercomputer, Crane, to the current directory (`.\`) of the
 your computer.
 
 
@@ -151,11 +151,11 @@ Usually it is convenient to upload and download files between your personal comp
 and the HCC supercomputers through a Graphic User Interface (GUI).
 Download and install the third party application **WinSCP**
 to connect the file systems between your personal computer and the HCC supercomputers. 
-Below is a step-by-step installation guide. Here we use the HCC cluster **Tusker**
-for demonstration. To use the **Crane** cluster, replace `tusker.unl.edu`
-with `crane.unl.edu`.
+Below is a step-by-step installation guide. Here we use the HCC cluster **Crane**
+for demonstration. To use the **Rhino** cluster, replace `crane.unl.edu`
+with `rhino.unl.edu`.
 
-1.  On the first screen, type `tusker.unl.edu` for Host name, enter your
+1.  On the first screen, type `crane.unl.edu` for Host name, enter your
     HCC account username and password for User name and Password. Then
     click on **Login**.
 

content/handling_data/data_storage/_index.md

@@ -37,7 +37,7 @@ environmental variable (i.e. '`cd $COMMON`')
 
 The common directory operates similarly to work and is mounted with
 **read and write capability to worker nodes all HCC Clusters**. This
-means that any files stored in common can be accessed from Crane and Tusker, making this directory ideal for items that need to be
+means that any files stored in common can be accessed from Crane and Rhino, making this directory ideal for items that need to be
 accessed from multiple clusters such as reference databases and shared
 data files.
 

content/handling_data/data_transfer/globus_connect/globus_command_line_interface.md

@@ -75,14 +75,14 @@ can now transfer and manipulate files on the remote endpoint.
 {{% notice info %}}
 To make it easier to use, we recommend saving the UUID number as a bash
 variable to make the commands easier to use. For example, we will
-continue to use the above endpoint (Tusker) by assigning its UUID code
-to the variable \`tusker\` as follows:
+continue to use the above endpoint (Crane) by assigning its UUID code
+to the variable \`crane\` as follows:
 {{< figure src="/images/21073499.png" >}}
 
 This command must be repeated upon each new login or terminal session
 unless you save these in your environmental variables. If you do not
 wish to do this step, you can proceed by placing the correct UUID in
-place of whenever you see \`$tusker\`.
+place of whenever you see \`$crane\`.
 {{% /notice %}}
   
 ---
@@ -98,7 +98,7 @@ command:
 
 To make a directory on the remote endpoint, we would use the \`globus
 mkdir\` command. For example, to make a folder in the users work
-directory on Tusker, we would use the following command:
+directory on Crane, we would use the following command:
 {{< figure src="/images/21073501.png" >}}
 
 To rename files on the remote endpoint, we can use the \`globus rename\`
@@ -112,14 +112,14 @@ command:
 All transfers must take place between Globus endpoints. Even if you are
 transferring from an endpoint that you are already connected to, that
 endpoint must be activated in Globus. Here, we are transferring between
-Crane and Tusker. We have activated the Crane endpoint and saved its
-UUID to the variable $crane as we did for $tusker above.
+Crane and Rhino. We have activated the Crane endpoint and saved its
+UUID to the variable $crane as we did for $crane above.
 
 To transfer files, we use the command \`globus transfer\`. The format of
 this command is \`globus transfer &lt;endpoint1&gt;:&lt;file\_path&gt;
 &lt;endpoint2&gt;:&lt;file\_path&gt;\`. For example, here we are
 transferring the file \`testfile.txt\` from the home directory on Crane
-to the home directory on Tusker:
+to the home directory on Crane:
 {{< figure src="/images/21073505.png" >}}
 
 You can then check the status of a transfer, or delete it all together,
@@ -129,7 +129,7 @@ using the given Task ID:
 To transfer entire directories, simply specify a directory in the file
 path as opposed to an individual file. Below, we are transferring the
 \`output\` directory from the home directory on Crane to the home
-directory on Tusker:
+directory on Crane:
 {{< figure src="/images/21073507.png" >}}
 
 For additional details and information on other features of the Globus