fix broken links, typos

ISUgenomics · Jul 9, 2024 · 18c593c · 18c593c
1 parent 82aa0a7
commit 18c593c
Show file tree

Hide file tree

Showing 10 changed files with 10 additions and 10 deletions.
diff --git a/_collection-base/02-computing-machine/03b-installations-windows.md b/_collection-base/02-computing-machine/03b-installations-windows.md
@@ -22,7 +22,7 @@ attributes: ["installation"]
 
 # Introduction
 
-This is a guide for setup of a windows machine for bioinformatics data analysis. I list here some important tools useful for most bioinformatics analyses and the process to install them. Check out the <a class="t-links" href="900">Project Management</a>.
+This is a guide for setup of a windows machine for bioinformatics data analysis. I list here some important tools useful for most bioinformatics analyses and the process to install them. Check out the <a class="t-links" href="900">Project Management</a> guide.
 
 ## General guide to software installation
 

diff --git a/_collection-base/04-devel-environment/01-integrated-development-environment.md b/_collection-base/04-devel-environment/01-integrated-development-environment.md
@@ -31,4 +31,4 @@ IDEs include many different tools that help developers code efficiently:
 * Application testing and deployment
 
 
-IDEs are essential tools for software development, provide one place to work on all aspects of a project, and have a wide range of features to streamline the development process. Some popular IDEs are [Visual Studio Code ⤴](01A-tutorial-VSCode.md), Eclipse, [PyCharm ⤴](02E-pycharm-ide.md), [Jupyter ⤴](01B-jupyter-basics), [RStudio ⤴](03A-rstudio-basics.md), Atom, and Spyder.
+IDEs are essential tools for software development, provide one place to work on all aspects of a project, and have a wide range of features to streamline the development process. Some popular IDEs are <a class="t-links" href="411"></a>, Eclipse, <a class="t-links" href="427"></a>, <a class="t-links" href="412"></a>, <a class="t-links" href="431"></a>, Atom, and Spyder.
diff --git a/_collection-base/04-devel-environment/03-r-programming-environment.md b/_collection-base/04-devel-environment/03-r-programming-environment.md
@@ -135,6 +135,6 @@ For example, you can use the `plot()` function to create a scatterplot:
 ```
 ![R_plot]({{ images_path }}/R_plot.png)
 
-<div class="protip" markdown="1">
+<div class="note" markdown="1">
 With its powerful statistical and data visualization capabilities, R is a valuable tool for anyone working with data.
 </div>
diff --git a/...on-base/06-hpc/01-hpc-networks/01-access-former-xsede/01-supercomputer-intro.md b/...on-base/06-hpc/01-hpc-networks/01-access-former-xsede/01-supercomputer-intro.md
@@ -21,7 +21,7 @@ attributes: ["user-guide"]
 
 # Introduction to ACCESS
 
-<div class="warning" markdown="1">
+<div class="note" markdown="1">
 **ACCESS has now replaced a similar service called the Extreme Science and Engineering Discovery Environment (XSEDE).** Similar to ACCESS, XSEDE was a NSF funded collection of supercomputers and high-end visualization and data analysis resources. XSEDE ended on August 31, 2022. <base class="mb">
 <button class="btn more mr"></button>Links to archives with more information about XSEDE are available <a href="https://portal.xsede.org/#/guest" target="_blank">here ⤴</a>.
 </div>

diff --git a/...tion-base/06-hpc/01-hpc-networks/01-access-former-xsede/02-supercell-storage.md b/...tion-base/06-hpc/01-hpc-networks/01-access-former-xsede/02-supercell-storage.md
@@ -22,7 +22,7 @@ attributes: ["user-guide", "command"]
 # Introduction
 
 <div class="warning" markdown="1">
-**XSEDE has been replaced by ACCESS.** Check the [ACCESS guide ⤴](01-supercomputer-intro.md) for more information.
+**XSEDE has been replaced by ACCESS.** Check the <a class="t-links" href="611.1"></a> for more information.
 </div>
 
 

diff --git a/_collection-base/06-hpc/01-hpc-networks/03-isu-hpc/01-isu-hpc-intro.md b/_collection-base/06-hpc/01-hpc-networks/03-isu-hpc/01-isu-hpc-intro.md
@@ -47,7 +47,7 @@ attributes: ["user-guide"]
 # Logging in
 To log in to Nova/Condo Clusters, you need to be connected to ISU network on-campus or use <a href="https://vpn.iastate.edu/+CSCOE+/logon.html#form_title_text" target="_blank">ISU VPN ⤴</a> if you are off-campus. The first time you try to log in to Nova or Condo, a new Google Authenticator (GA) account is created. You will need to use GA for login.
 
-The first time you use the <a class="t-links" href="623"></a> connection to Nova/Condo, it will respond with:
+The first time you use the <a class="t-links" href="623"></a> to Nova/Condo, it will respond with:
 
 <pre class="output">
 "host key not found, generate hostkey?(yes/no)"

diff --git a/_collection-base/06-hpc/01-hpc-networks/03-isu-hpc/02-isu-hpc-condo-cluster.md b/_collection-base/06-hpc/01-hpc-networks/03-isu-hpc/02-isu-hpc-condo-cluster.md
@@ -34,7 +34,7 @@ attributes: ["user-guide", "command"]
 If logging in the first time, check the <a class="t-links" href="613.1" section="#logging-in">Logging in</a> section of intro to HPC page.
 </div>
 
-Using Condo cluster has same requirements as the [Nova Computing Cluster ⤴](03-isu-hpc-nova-cluster) except Condo is free. Faculty can fill out the Cluster Access Request on <a href="https://www.hpc.iastate.edu/" target="_blank">HPC webpage ⤴</a> to request access for their group. Use Google Authenticator on <a href="https://www.hpc.iastate.edu/guides/condo-2017/access-and-login/google-auth-on-android" target="_blank">Android ⤴</a>, <a href="https://www.hpc.iastate.edu/guides/condo-2017/access-and-login/google-auth-on-iphone-ipad-ipod" target="_blank">iPhone ⤴</a> or <a href="https://www.hpc.iastate.edu/guides/condo-2017/access-and-login/google-auth-on-windows" target="_blank">Windows ⤴</a> devices for authentication.
+Using Condo cluster has same requirements as the <a class="t-links" href="613.3"></a> except Condo is free. Faculty can fill out the Cluster Access Request on <a href="https://www.hpc.iastate.edu/" target="_blank">HPC webpage ⤴</a> to request access for their group. Use Google Authenticator on <a href="https://www.hpc.iastate.edu/guides/condo-2017/access-and-login/google-auth-on-android" target="_blank">Android ⤴</a>, <a href="https://www.hpc.iastate.edu/guides/condo-2017/access-and-login/google-auth-on-iphone-ipad-ipod" target="_blank">iPhone ⤴</a> or <a href="https://www.hpc.iastate.edu/guides/condo-2017/access-and-login/google-auth-on-windows" target="_blank">Windows ⤴</a> devices for authentication.
 
 
 To log in to Condo, use any Terminal (Terminal on Linux/Mac and Powershell on Windows) to ssh with the login hostname:

diff --git a/_collection-base/06-hpc/01-hpc-networks/03-isu-hpc/03-isu-hpc-nova-cluster.md b/_collection-base/06-hpc/01-hpc-networks/03-isu-hpc/03-isu-hpc-nova-cluster.md
@@ -44,7 +44,7 @@ Once connected to ISU network, use any Terminal (Terminal on Linux/Mac and Power
 ## Data Transfer and Jobs
 
 <div class="required" markdown="1">
-**Nova transfer node:** @nova.its.iastate.edu
+**Nova transfer node:** @novadtn.its.iastate.edu
 </div>
 <div class="protip" markdown="1">
 Use the login hostname @**nova**.its.iastate.edu to log in to Nova and submit jobs, <br>

diff --git a/_collection-base/06-hpc/01-hpc-networks/03-isu-hpc/04-isu-hpc-lss-storage.md b/_collection-base/06-hpc/01-hpc-networks/03-isu-hpc/04-isu-hpc-lss-storage.md
@@ -25,7 +25,7 @@ The LSS is a storage service for Iowa State faculty and staff. It is useful for
 
 ## Access
 
-Space on LSS can be requested from <a href="https://lss.apps.it.iastate.edu/" target="_blank">ISU LSS website ⤴</a>. <base class="mb">
+Space on LSS can be requested from <a href="https://lss.apps.it.iastate.edu/" target="_blank">ISU LSS website ⤴</a> (requires ISU login). <base class="mb">
 Once you have purchased space on LSS, folders can be mounted to your computer directly. Check out this guide on <a href="https://researchit.las.iastate.edu/guides/lss/mount_folders/" target="_blank">how to mount folders from LSS ⤴</a>.
 
 

diff --git a/_collection-base/06-hpc/07-containers/02-docker/01-docker-basics.md b/_collection-base/06-hpc/07-containers/02-docker/01-docker-basics.md
@@ -34,7 +34,7 @@ Containers are executable units of software containing anything from a small pro
 
 Apptainer *(previous Singularity)* is commonly used for High-Performance Computing (HPC) environments whereas Docker is usually run locally as it needs <a class="t-links" href="324">admin privileges</a>. Docker container images can be searched from the <a href="https://hub.docker.com/search?q=" target="_blank">Docker Hub ⤴</a> or directly from the Docker Desktop app. <br>
 
-<div class="note" markdown="1">
+<div class="protip" markdown="1">
 Apptainer *(previous Singularity)* is able to support Docker containers, which means that **you can run Docker containers using Apptainer**. But, Docker does not natively support Apptainer/Singularity containers. However, there are some workarounds that allow you to run Apptainer containers inside a Docker container, such as using Apptainer as an entry point for the Docker container.
 </div>