From 9ffc13bd1662ee0ef43cae10464581526ed4abc2 Mon Sep 17 00:00:00 2001 From: Johan Gustafsson Date: Wed, 11 Feb 2026 16:48:58 +1030 Subject: [PATCH 01/20] update scss and _config.yml --- _config.yml | 3 +- _sass/_bootstrap_variables.scss | 2 +- _sass/_custom_classes.scss | 52 +++++++++++++++++++++++++++++++-- 3 files changed, 53 insertions(+), 4 deletions(-) diff --git a/_config.yml b/_config.yml index 5334632..2262294 100755 --- a/_config.yml +++ b/_config.yml @@ -2,7 +2,7 @@ title: ABLeS topnav_title: ABLeS description: ABLeS -remote_theme: ELIXIR-Belgium/elixir-toolkit-theme@5.0.0 +remote_theme: ELIXIR-Belgium/elixir-toolkit-theme permalink: pretty gtag: G-T8GWK081T9 @@ -21,6 +21,7 @@ defaults: path: "" type: "pages" values: + permalink: /:basename layout: "page" sidebar: main diff --git a/_sass/_bootstrap_variables.scss b/_sass/_bootstrap_variables.scss index 66ca52e..bcb3575 100644 --- a/_sass/_bootstrap_variables.scss +++ b/_sass/_bootstrap_variables.scss @@ -14,7 +14,7 @@ $nav-link-hover-color: $primary; $link-color: $blue; $navbar-dark-color: $white; $navbar-dark-hover-color: $white; -$navbar-light-hover-color: $light; +$navbar-light-hover-color: $primary; $link-color: #205a86; $nav-link-color: $white; $nav-link-hover-color: $light; diff --git a/_sass/_custom_classes.scss b/_sass/_custom_classes.scss index 68de6ef..d6a2c35 100644 --- a/_sass/_custom_classes.scss +++ b/_sass/_custom_classes.scss @@ -13,6 +13,15 @@ img { @extend .img-fluid; } +h1 { + font-size: 2.4rem; + font-weight: bolder; +} + +h2 { + font-size: 1.7rem; + font-weight: bolder; +} .accordion-button:not(.collapsed) { color:#FFFFFF; @@ -28,7 +37,7 @@ img { header .navbar { .navbar-brand { font-size: 2.25rem; - //color: $white !important; + color: $black !important; img { max-height: 80px; } @@ -59,4 +68,43 @@ header .navbar { background-color: #5ac3b1; } } -} \ No newline at end of file +} + +.navbar-nav .nav-item > a { + &.active { + color: $white; + background-color: $primary; + border-radius: $border-radius; + } +} + + +.index-main-container { + display: flex; + flex-wrap: wrap; +} + +.index-panel { + padding: 20px; + flex: 1; + min-width: 300px; +} + +.index-left-panel { + flex: 1; +} + +.index-right-panel { + flex: 1.5; +} + +.video-wrapper { + width: 100%; + aspect-ratio: 16 / 9; +} + +.video-wrapper iframe { + width: 100%; + height: 100%; + border-radius: 8px; +} From fed9bd9db8aca3b7e9c08d26c0fb8ffd36d1b8cf Mon Sep 17 00:00:00 2001 From: Johan Gustafsson Date: Wed, 11 Feb 2026 16:50:14 +1030 Subject: [PATCH 02/20] update acknowledgements.md and if89.md --- acknowledgements.md | 2 +- if89.md | 57 +++++++++++---------------------------------- 2 files changed, 15 insertions(+), 44 deletions(-) diff --git a/acknowledgements.md b/acknowledgements.md index cd56043..d038dfb 100755 --- a/acknowledgements.md +++ b/acknowledgements.md @@ -37,4 +37,4 @@ Gustafsson, Ove Johan Ragnar, Al Bkhetan, Ziad, Francis, Rhys & Manos, Steven. ( Authorship is NOT expected for routine / simple services provided (e.g. tool installation) and an acknowledgement is sufficient in these cases. We approach authorship issues with a generous spirit and aim to fairly attribute contributions. -In some cases, it may be appropriate for ABLeS support staff, or specialists at NCI or Pawsey to be co-authors on publications. Examples of this include when these specialists provide significant input into the publication, including a significant contribution to method / protocol / pipeline development, study design, data and results analysis, or interpretation. +In some cases, it may be appropriate for ABLeS support staff, or specialists at NCI or Pawsey, to be co-authors on publications. Examples of this include when these specialists provide significant input into the publication, including a significant contribution to method / protocol / pipeline development, study design, data and results analysis, or interpretation. diff --git a/if89.md b/if89.md index ba78164..e0c60f1 100755 --- a/if89.md +++ b/if89.md @@ -5,7 +5,9 @@ toc: false This page provides a comprehensive overview of tools, containers, workflows, and datasets available to ABLeS researchers. It also includes information about the **Australian BioCommons Tools and Workflows project (if89)**, which serves as a shared repository for bioinformatics tools and workflows. -### Pawsey Supercomputing Centre + +## Pawsey Supercomputing Centre + #### Software @@ -13,22 +15,27 @@ There is a wide range of centrally installed software for Setonix users, includi Setonix users can also install their choice of software on the `/software` partition. We also encourage usage of containers with Singularity. Users are able to download any containers they like! + #### Reference datasets Popular bioinformatics [reference datasets](https://support.pawsey.org.au/documentation/display/US/Life+Science+and+Bioinformatics) are available on Pawsey. Additional reference sets can be requested via -### National Computational Infrastructure (NCI) -#### Centrally supported software (`/apps`) +## National Computational Infrastructure (NCI) + -Centrally supported software available through NCI can be viewed [here](https://opus.nci.org.au/display/Help/5.+Software+Applications). +#### Centrally supported software: `/apps` -### Shared repository of tools and software (`project if89` on NCI) +Centrally supported software available through NCI can be [**viewed here**](https://opus.nci.org.au/display/Help/5.+Software+Applications). -Users at NCI also have access to the `Australian BioCommons Tools and Workflows project`, in project allocation `if89`. This is a repository of popular tools, containers and workflows that can be used by anyone in the NCI system. + +#### Shared repository of tools and software: `project if89` + +All NCI users can also join the `Australian BioCommons Tools and Workflows project`: in project allocation `if89`. This is a repository of popular software tools, containers, and workflows that can be used by anyone in the NCI system. Anyone from an NCI project is also invited to contribute to `if89`, and add more software installations that can be shared with others. + #### Software The list of tools available through the Australian BioCommons Shared Tools and Workflows repository (`NCI (if89)`) is available through ToolFinder. @@ -79,43 +86,6 @@ The list of tools available through the Australian BioCommons Shared Tools and W
-#### Containers - -
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-

- -

-
-
- Will be available soon. -
-
-
-
- -
- -#### Workflows - -
-
-

- -

-
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- Will be available soon. -
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- -
#### Software databases @@ -253,6 +223,7 @@ A list of the currently available (`as of 25 Aug 2025`) databases is included be

+ ## if89 Contributors {% include contributor-tiles-all.html custom="Hardip Patel, J King Chang, Ziad Al Bkhetan, Andre Martins Reis, Hasindu Gamaarachchi, Kyle Drover, Tim Amos, Leah Kemp, Kisaru Liyanage, Terry Bertozzi, Javed Shaikh, Kirat Alreja, Andrey Bliznyuk, Hyungtaek Jung, Wenjing Xue, Farhad Masoomi-Aladizgeh, Haixia Guan, Johan Gustafsson, Dale Roberts" sort=false%} From b65bdf4bb394beb2cf823fefcf416ade0f9a1296 Mon Sep 17 00:00:00 2001 From: Johan Gustafsson Date: Wed, 11 Feb 2026 16:52:33 +1030 Subject: [PATCH 03/20] update ymls --- _data/footer.yml | 3 +-- _data/sidebars/main.yml | 20 +++++++++++++------- _data/topnav.yml | 5 +++++ 3 files changed, 19 insertions(+), 9 deletions(-) create mode 100644 _data/topnav.yml diff --git a/_data/footer.yml b/_data/footer.yml index f57db3d..28fd64a 100644 --- a/_data/footer.yml +++ b/_data/footer.yml @@ -1,6 +1,5 @@ # see https://github.com/ELIXIR-Belgium/elixir-toolkit-theme -copyright: 'This site uses cookies to help the website run effectively. To find out more, read our [cookies](https://www.biocommons.org.au/cookies) statement.' -extra_line: ABLeS is subject to the Australian BioCommons [Code of Conduct](https://doi.org/10.5281/zenodo.4276854) and [Privacy Policy](https://www.biocommons.org.au/privacy). +copyright: 'This site uses cookies to help the website run effectively. To find out more, read our [cookies](https://www.biocommons.org.au/cookies) statement. ABLeS is subject to the Australian BioCommons [Code of Conduct](https://doi.org/10.5281/zenodo.4276854) and [Privacy Policy](https://www.biocommons.org.au/privacy).' columns: - type: image image_width: 320px diff --git a/_data/sidebars/main.yml b/_data/sidebars/main.yml index 6719c44..4bacc12 100644 --- a/_data/sidebars/main.yml +++ b/_data/sidebars/main.yml @@ -2,16 +2,22 @@ subitems: - title: Home url: /index + - title: About + url: /about - title: News & events url: /news-events - - title: Eligibility - url: /eligibility - title: Getting started - url: /projects_allocations - - title: Resources & Training - url: /resources - - title: Available software and data - url: /if89 + subitems: + - title: Eligibility + url: /eligibility + - title: Projects + url: /projects_allocations + - title: Resources & Training + url: /resources + - title: Available software and data + url: /if89 + - title: Sharing project outputs + url: sharing - title: ABLeS participants url: /participants - title: Acknowledging ABLeS diff --git a/_data/topnav.yml b/_data/topnav.yml new file mode 100644 index 0000000..2810b79 --- /dev/null +++ b/_data/topnav.yml @@ -0,0 +1,5 @@ +#subitems: +#- title: About +# url: /about +#- title: News & Events +# url: /news-events From 1590a8180b6917d32422bc49e5a4e44f6e6fdb51 Mon Sep 17 00:00:00 2001 From: Johan Gustafsson Date: Wed, 11 Feb 2026 16:53:17 +1030 Subject: [PATCH 04/20] update Gemfile and team.md --- Gemfile | 2 ++ team.md | 2 +- 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/Gemfile b/Gemfile index 889eaec..ef72f9f 100755 --- a/Gemfile +++ b/Gemfile @@ -5,6 +5,8 @@ gem "webrick", "~> 1.8.1" gem "jekyll", "~> 4.3.2" gem "jemoji", "~> 0.13.0" gem "kramdown-parser-gfm", "~> 1.1" +gem "csv" +gem "openssl", "~> 3.3.1" group :jekyll_plugins do gem "jekyll-redirect-from", "~> 0.16.0" diff --git a/team.md b/team.md index d7450c9..342b5d8 100644 --- a/team.md +++ b/team.md @@ -1,5 +1,5 @@ --- -title: ABLeS Team +title: Meet the Team toc: false --- From ad4e396b490b3d6f4e6999ebb08763eb4cc87c6f Mon Sep 17 00:00:00 2001 From: Johan Gustafsson Date: Wed, 11 Feb 2026 16:54:49 +1030 Subject: [PATCH 05/20] update contact-us.md --- contact-us.md | 38 ++++++++++++++++++++++++++++++-------- 1 file changed, 30 insertions(+), 8 deletions(-) diff --git a/contact-us.md b/contact-us.md index 45b859e..783c189 100755 --- a/contact-us.md +++ b/contact-us.md @@ -2,11 +2,33 @@ title: Help and Contact Details --- -| **Type of problem / challenge / issue** | **Contact details** | -|----------------------------------------------------------------------------------------------|---------------------------------------------------------------------------------------| -| Compute system issues at the NCI | Email:

| -| Compute system issues at Pawsey | Email:

| -| Questions about the ABLeS program | Email:

| -| Requesting tool installations | Please use the [ABLeS GoogleForm](https://docs.google.com/forms/d/e/1FAIpQLScpiyqERdxw6gMxjlq_CkiI3qvJ60YaeWHKTJChMjcnv8aBBA/viewform?usp=sf_link) | -| Reporting challenges with a specific bioinformatics workflow, or requesting assistance with this workflow | Please use the [ABLeS GoogleForm](https://docs.google.com/forms/d/e/1FAIpQLSere1PvgPEuJkpvQUk1-11C88IAeQNQKEUFc-Qgbn5GgKK2jw/viewform?usp=sf_link) | -| Any other issue | Email:

| + +#### Issues with compute systems + +For **NCI**, email Ziad and the NCI helpdesk. + +``` +ziad@biocommons.org.au +help@nci.org.au +``` + +For **Pawsey**, email Ziad and the Pawsey helpdesk. + +``` +ziad@biocommons.org.au +help@pawsey.org.au +``` + + +#### Requesting tool installations + +Complete the [**GoogleForm here**](https://docs.google.com/forms/d/e/1FAIpQLScpiyqERdxw6gMxjlq_CkiI3qvJ60YaeWHKTJChMjcnv8aBBA/viewform?usp=sf_link). + + +#### Questions about the ABLeS program, and any other issue + +Email the ABLeS team. + +``` +ables@biocommons.org.au +``` From 384b8d1c58a2440be41a9998d5ef8890eca72a24 Mon Sep 17 00:00:00 2001 From: Johan Gustafsson Date: Wed, 11 Feb 2026 16:56:30 +1030 Subject: [PATCH 06/20] update if89-technical.md --- if89-technical.md | 27 +++++++++++++++++++-------- 1 file changed, 19 insertions(+), 8 deletions(-) diff --git a/if89-technical.md b/if89-technical.md index 47a16d8..f22387b 100755 --- a/if89-technical.md +++ b/if89-technical.md @@ -1,5 +1,6 @@ --- -title: ABLeS - Application Installation Guidelines +title: Project if89 software installation guidelines +contributors: [Dale Roberts, Johan Gustafsson, Ziad Al Bkhetan, Hardip Patel] --- ## Introduction @@ -18,6 +19,7 @@ For each software, an installation script should be created to install the softw This helps to automate the process when a reinstallation is required. This script should be added to the repository of all scripts and patches, which is available at: [https://git.nci.org.au/dsr900/ables-software-installations](https://git.nci.org.au/dsr900/ables-software-installations). This script repository follows the same file structure as the NCI `/apps` directory which is `//`. + ## Prerequisites In order to contribute to `if89`, you need to satisfy the following conditions: @@ -30,6 +32,7 @@ In order to contribute to `if89`, you need to satisfy the following conditions: * Ziad Al Bkhetan: * Javed Shaikh: + ## General guidelines These are some general guidelines to be aware of before installing any software: @@ -51,6 +54,7 @@ This will create a ‘fat binary’ that contains optimised code for all listed `$ g{cc,++,fortran} -march=broadwell ...` 8. Module and/or common files must also be created by the installation script. + ## First-time installation procedure Before installing any software, make sure the software is not already installed into `/g/data/if89/apps/` as well as into NCI supported apps `/apps/`. @@ -69,7 +73,8 @@ The procedure consists of three main stages: 2. Install the software on the `if89` project 3. Add the installation script to the `ABLeS-software-repository` -**Details are below** + +### Details are below 1. Clone `ables-software-installations` If you have done this step before, jump to step 2. If this is your first time adding to `if89`, you will need to clone the `ables-software-installations` repository from [https://git.nci.org.au/dsr900/ables-software-installations](https://git.nci.org.au/dsr900/ables-software-installations). Access is managed through your Gadi username and password. @@ -85,6 +90,8 @@ The procedure consists of three main stages: git clone https://git.nci.org.au/dsr900/ables-software-installations.git ``` +{:start="2"} + 2. Make sure that the local repository is up to date before starting work on any new package. A branch must be created from the latest version of the ‘main’ branch of the repository. Change `APP_NAME` and `APP_VERSION` according to the software you are installing. ~~~ @@ -97,6 +104,8 @@ The procedure consists of three main stages: git checkout -b ${APP_NAME}/${APP_VERSION} ~~~ +{:start="3"} + 3. Create a directory for the app and its version following the same file structure as other apps. Copy the install script template to the directory and rename it to install.sh. Make sure that the file is executable. @@ -109,6 +118,8 @@ The install template is available directly under the root directory of `ables-so chmod u+x ./install.sh ~~~ +{:start="4"} + 4. We recommend using other paths for testing as mentioned in the template file. You can use the same file paths mentioned there for testing until you are happy with the installation, then use the original paths. Details are in the template file. 5. Edit the install file according to the app you are installing according to the tips provided within the install template. 6. Run the install.sh script to do the final installation. Make sure the paths are configured to contain the final values not the testing ones. @@ -117,6 +128,8 @@ The install template is available directly under the root directory of `ables-so ./install.sh ~~~ +{:start="7"} + 7. Make sure you clean up the directory * only install.* and installation related files if they exist should be kept) and only keep the installation files needed to be pushed to the repository. * Then commit your changes (should be adding install.sh file) and merge the branch you created with the main branch. @@ -132,12 +145,14 @@ The install template is available directly under the root directory of `ables-so git push ~~~ + ## Modifying existing installations * If an app installation needs to be altered after being made generally available, an update script needs to be added to the repository in the same directory as the installation script of the application being modified, and the same branch-merge procedure must be followed. * The update script should be named `update.*` and the same update script will not be run twice. It is recommended to give the update script a descriptive name e.g. `update.shortdescription.sh`. * The database of installations maintained by the installer tool will record the order in which update scripts were run, so in cases of disaster recovery, the current state of an application in the installation area will be able to be reconstructed by running `install.sh`, then all `update.*` scripts in a given `/` directory chronologically. + ## When scripted installations are not possible If scripted installations are not possible, sufficient documentation needs to be available such that the installation can be performed consistently by any `if89` maintainer. @@ -148,6 +163,7 @@ Please contact ABLeS team if you have such case. * An installation script is still required, however, all it needs to do is untar the completed installation from the staging area into `/g/data/if89/apps`. * Examples of acceptable manual installations are when GUI installers are required, or when pre-built software must be retrieved from behind an authenticated web service. + ## Installation script standards A few general rules need to be followed in order for the installation repository and python tool to work together cohesively. @@ -168,6 +184,7 @@ They are as follows: * Any software that is identified only by a date stamp should use `YYYYMMDD` format to allow version comparison extensions to work correctly. * Avoid `/--