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/_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/_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/tiles.yml b/_data/tiles.yml new file mode 100644 index 0000000..7175b83 --- /dev/null +++ b/_data/tiles.yml @@ -0,0 +1,48 @@ +- title: "Request a new project" + type: new + url: https://docs.google.com/forms/d/e/1FAIpQLScTzDsJeLxB9if4PnuOiDsDCtSESKTc5d39rDSTUGu5fjCw3Q/viewform?usp=header +- title: "Request additional resources" + type: existing + url: https://docs.google.com/forms/d/e/1FAIpQLSe_zrqiE7QSh1FFlmzMxFV6F_u5G-4dnAJ1H7vpN6kkkATyww/viewform?usp=header +- title: "Request software installation" + type: existing + url: https://docs.google.com/forms/d/e/1FAIpQLScpiyqERdxw6gMxjlq_CkiI3qvJ60YaeWHKTJChMjcnv8aBBA/viewform?usp=sf_link +- title: "Request general help" + type: existing + url: https://docs.google.com/forms/d/e/1FAIpQLSere1PvgPEuJkpvQUk1-11C88IAeQNQKEUFc-Qgbn5GgKK2jw/viewform?usp=sf_link +- title: "Report project outcome" + type: existing + url: https://docs.google.com/forms/d/e/1FAIpQLSdO1w-RY8OexUBwJx8BHNMwSRNPA3_-5r6pefdQW8ancbKZqw/viewform?usp=sf_link +- title: "See available tools" + type: new + url: /resources#3-collectively-maintained-software-and-reference-data-project-if89 +- title: "Help, this is the first time I'm requesting an ABLeS project" + type: new + url: /eligibility +- title: "General software" + type: sharing + url: /sharing#general-software +- title: "Computational workflows" + type: sharing + url: /sharing#workflows +- title: "Reference data" + type: sharing + url: /sharing#reference-data +- title: "SOPs and protocols" + type: sharing + url: /sharing#sops-and-protocols +- title: "Pawsey user training" + url: https://pawsey.atlassian.net/wiki/spaces/US/pages/51917528/User+Training + type: pawsey +- title: "Setonix user guide" + url: https://pawsey.atlassian.net/wiki/spaces/US/pages/51925434/Setonix+User+Guide + type: pawsey +- title: "Calendar of upcoming training opportunities" + url: https://opus.nci.org.au/display/Help/NCI+Training+and+Educational+Events + type: nci +- title: "User guides" + url: https://opus.nci.org.au/ + type: nci +- title: "Register to become a NCI user" + url: + type: nci \ No newline at end of file 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 diff --git a/_includes/affiliation-tiles-selection_mod.html b/_includes/affiliation-tiles-selection_mod.html new file mode 100644 index 0000000..8ca7dc1 --- /dev/null +++ b/_includes/affiliation-tiles-selection_mod.html @@ -0,0 +1,15 @@ +{%- assign alllogos = site.data.affiliations %} +
+ {%- assign filtered_logos = alllogos | where: "type", include.type %} + {%- for affiliation in filtered_logos %} + {%- if affiliation.image_url and affiliation.expose == true %} +
+
+
+ {% if affiliation.url %}{% endif %}{{ affiliation.name }}{%- if affiliation.url %}{% endif %} +
+
+
+ {%- endif %} + {%- endfor %} +
\ No newline at end of file diff --git a/_includes/events.html b/_includes/events.html index f70d212..00960d6 100644 --- a/_includes/events.html +++ b/_includes/events.html @@ -8,7 +8,7 @@

Events

{%- assign current_date = "now" | date: "%s" -%}
-

Upcoming

+ {%- assign events = site.data.events | sort: 'date' -%} {%- assign count = 0 -%}
@@ -39,7 +39,7 @@

{{ event.name | escape }}

- + diff --git a/_includes/tiles.html b/_includes/tiles.html new file mode 100644 index 0000000..155f3a7 --- /dev/null +++ b/_includes/tiles.html @@ -0,0 +1,72 @@ +{% comment %} +include source was modified from that available at https://github.com/Australian-Structural-Biology-Computing/australian-structural-biology-computing.github.io/blob/2ad8159cddd12b3ec4dfbf33fbbf310af9d686ba/_includes/section-navigation-tiles_mod.html +{% endcomment %} + +{%- assign links_to_add_as_tiles = site.data.tiles -%} +
+
+
+ {%- for item in links_to_add_as_tiles -%} + {%- if item.type == include.type -%} + +
+
+

{{ item.title }}

+
+
+ + {%- endif -%} + {%- endfor -%} +
+
+
+ + \ No newline at end of file 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; +} diff --git a/about.md b/about.md new file mode 100755 index 0000000..10afdf2 --- /dev/null +++ b/about.md @@ -0,0 +1,31 @@ +--- +title: About +toc: false +--- + +The ABLeS (Australian BioCommons Leadership Share) program was established in April 2021 to more readily support data-driven bioinformatics. This effort is supported by [Australian BioCommons](https://www.biocommons.org.au/) in partnership with [Bioplatforms Australia](https://bioplatforms.com/), the [National Computational Infrastructure (NCI, Canberra)](https://nci.org.au/), and the [Pawsey Supercomputing Research Centre (Pawsey, Perth)](https://pawsey.org.au/). + +ABLeS offers access to: + +- computational and data infrastructure; +- specialized expertise; +- support on adopting best practices and effectively sharing outputs; +- a community-driven repository of bioinformatics software, including tools and workflows. + +If you want to read more about ABLeS, more details are available in the ABLeS publication: + +*Gustafsson, Ove Johan Ragnar, Al Bkhetan, Ziad, Francis, Rhys & Manos, Steven. (2023). Enabling national step changes in bioinformatics through ABLeS, the Australian BioCommons Leadership Share (3.0). Zenodo. [https://doi.org/10.5281/zenodo.10139651](https://doi.org/10.5281/zenodo.10139651)* +
+ + + +## Acknowledgements + +ABLeS is co-funded by Bioplatforms Australia, the National Computational Infrastructure (NCI) and Pawsey Supercomputing Research Centre. This program forms part of the national Australian BioCommons infrastructure. + +
+ + +{% include affiliation-tiles-selection_mod.html type="infrastructure" %} + + diff --git a/acknowledgements.md b/acknowledgements.md index cd56043..dc31c36 100755 --- a/acknowledgements.md +++ b/acknowledgements.md @@ -1,8 +1,10 @@ --- -title: Acknowledgements and Authorship +title: ABLeS Acknowledgment guidelines toc: false --- +Researchers who use ABLeS resources are expected to acknowledge ABLeS in any resulting publications, presentations, or research outputs. + ## Citing and acknowledging ABLeS The ABLeS program should be both cited and acknowledged in any publication, presentation or grant application that was supported by data or services provided by ABLeS. @@ -35,6 +37,20 @@ Gustafsson, Ove Johan Ragnar, Al Bkhetan, Ziad, Francis, Rhys & Manos, Steven. ( ## ABLeS co-authorship policy -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. +For routine or standard services (e.g. tool installation or access to compute infrastructure), a formal acknowledgement of ABLeS is sufficient. + +In some cases, co-authorship may be appropriate. + +This typically applies where ABLeS support staff or specialists at NCI or Pawsey have made a substantial intellectual contribution to the work, such as: +- Development or optimisation of methods, protocols, or pipelines +- Study design input +- Data or results analysis +- Interpretation of findings + +We approach authorship discussions collaboratively and in the spirit of fair and transparent attribution. + +## Share your outputs + +We encourage all projects to inform the ABLeS team of publications, software releases, datasets, and other outputs arising from ABLeS-supported work. Sharing outcomes helps demonstrate national impact and strengthens continued support for the community. -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. +Visit our [**Sharing project outputs** page](ables/sharing.md) to learn how to notify us and be featured. 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 +``` diff --git a/eligibility.md b/eligibility.md index 946467d..30d7766 100644 --- a/eligibility.md +++ b/eligibility.md @@ -5,100 +5,40 @@ toc: false ABLeS is available to research groups and bioinformatics communities across Australia. -Participants who wish to use ABLeS must ensure their projects align with ABLeS principles. - -## Principles of ABLeS projects - -ABLeS projects broadly align with the following three principles: - -1. Projects are life science related and contribute to producing and sharing data, research, or software-based outcomes. - -2. Project participants must have the necessary expertise to drive and execute the bioinformatics goals of their work. - -3. Projects must plan and utilize ABLeS resources responsibly, recognizing their status as finite and consumable. - -More details are provided in the table below: - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
PrincipleCharacteristicsProject Type
Reference DataProduction BioinformaticsSoftware Accelerator
Data centric outcomesProduction of reference and derived data assets that will be published to enable use / reuse by others outside the group.✓✓
Research centric outcomesProduction of data assets and outputs that are critical to research projects and consortia making use of best practice, production level bioinformatics approaches.✓
Software centric outcomesCreation, development, installation, testing and/or optimisation of software that will be made available for use / reuse by others in the life sciences community.✓
Common research themeA defined cross-institutional collaboration, project, community, consortium, or some other collaborative construct, that is focused on a common research theme.✓
Development & optimisationGroups work to understand their software, methods and the optimal approaches to solving the bioinformatics problems at hand. ABLeS will facilitate both the experimental / testing and production phases of computational analyses.✓
Planned usage of ABLeS resourcesThe use of ABLeS resources is planned and approached with a level of care appropriate to their status as limited and consumable resources.✓
SharingAppropriate mechanisms are used to share outputs that support and assist other groups, with examples provided in the ABLeS publication. Outputs include software, methods, training, resource usage and quality assessments for derived reference data sets, submissions to data international repositories and research publications.✓
- -## ABLeS expectations - -|Principle| Description| -|-------------|------------------------------------------------------------------| -|**Project leadership**| A project lead is responsible for all use of resources provided, which will need to adhere to relevant facility processes and policies. The lead will also monitor and manage reasonable usage of their project computational infrastructure allocations.| -|**Group-level decision making**| A collaborative decision making mechanism to prioritise the bioinformatics work using relevant computational resources must exist. This can be a formalised steering committee, a working group, or some other forum which is representative of the collaboration. Resources used must be agreed upon / in line with the community’s decision making mechanism and align with community priorities.| -|**Group-level expertise**|The community has expertise which will drive and execute its bioinformatics agenda. This expertise offers a strong collaboration link with the expertise and support available through ABLeS, NCI and Pawsey.| -|**Collaboration & consultation**|ABLeS is collaborative and involves BioCommons, the research community, and the computational facilities. It is also a standing item for discussion and forums play a strong role in managing the use of ABLeS: groups will thus engage with BioCommons in an open and collaborative manner, with regular meetups.| -|**Follow compute facility access policies**|All users must abide by the relevant access policies of Pawsey and NCI. [NCI Terms and Conditions of Access](https://nci.org.au/users/nci-terms-and-conditions-access); [NCI Data Collections Management](https://opus.nci.org.au/display/NDP/NCI+Data+Collections+and+Publishing); and [Pawsey Conditions of Access](https://support.pawsey.org.au/documentation/display/US/Conditions+of+Use).| -|**Time frame / duration of allocations**|Each project is reviewed at the 6 month mark, to ensure resources are being used as efficiently as practical and so challenges can be identified / addressed by the ABLeS team. Reference data and production projects are ongoing by definition, while software accelerator projects need to be renewed at 6 months if the work originally described for the project has not been completed.| +Read below to determine if your project aligns with our core principles and resource criteria: + +| Reference Data | Production Bioinformatics | Software Accelerator | +|--------------------------------------------|-------------------------------------------------------------------|-------------------------------------------------------------| +| You are creating high-quality data assets (e.g., a reference genome) intended for broad community reuse. | You are running established, best-practice pipelines for a large-scale research consortium. | You are developing, testing, or optimizing bioinformatics tools for the wider community. | + +## Core eligibility criteria + +To qualify, your project must meet the following three pillars: + +#### Pillar 1: Domain and Impact +- **Life Sciences focus**: Your work must be biological or medical in nature. +- **Open outputs**: You are committed to sharing your results (data, software, or methods) with the broader research community and ABLeS. (Read more abour this [here](ables/sharing.md)). + +#### Pillar 2: Technical Readiness +- **Internal expertise**: Your team must have the "hands-on" bioinformatics skills required to execute the work. +- **HPC readiness**: You are prepared to work within the NCI or Pawsey supercomputing environments. + +#### Pillar 3: Responsible Resource Use +- **Finite resources**: You acknowledge that HPC compute and storage are limited; you have a plan to use them efficiently. +- **Active management**: You agree to a 6-month progress review to ensure resources are being utilized effectively. + +## Governance and Leadership + +Every ABLeS project requires a clear leadership structure to ensure accountability: + +- **Project Lead**: one person is responsible for all resource usage and adherence to facility policies. + +- **Collaborative decision-making**: for larger groups, a steering committee or working group must be in place to allow collaborative decision making mechanism and align with community priorities. + +- **Compliance**: All users must abide by the [NCI Terms and Conditions](https://nci.org.au/users/nci-terms-and-conditions-access) and [Pawsey Conditions of Access](https://pawsey.atlassian.net/wiki/spaces/US/overview). + +- **Collaboration & consultation**: ABLeS is collaborative and involves BioCommons, the research community, and the computational facilities. It is also a standing item for discussion and forums play a strong role in managing the use of ABLeS: groups will thus engage with BioCommons in an open and collaborative manner, with regular meetups. + +## Is ABLeS the right fit for your research? +Take a 30-second self-assessment to see if your project aligns with the ABLeS criteria: click [here](https://docs.google.com/forms/d/e/1FAIpQLSe-WGVW3jOdvGm84jybu4T-CXaBd4w9L8Dq67YqyK7zSSKArw/viewform?usp=publish-editor). 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 `/--