Merge branch 'develop' into 'master'

[release] Regular merge of develop

See merge request R3/howto-cards!415

generator @ fe6de897

-Subproject commit 945abc75e44121be434587ec9b265dbee26d3792
+Subproject commit fe6de8977024b9ddfbc1a17df6e7ba8a0caf9c0f

cards.md

@@ -62,6 +62,7 @@ order: -1
 	<div class="index-box noborderbox" id="exchange-channels-card">
 		<h3>Exchange channels</h3>
 		<ul>
+			<li><a href="{{ 'external/exchange-channels/lft' | relative_url }}">LCSB file transfer (LFT) Quick Guide</a></li>
 			<li><a href="{{ 'external/exchange-channels/calendar' | relative_url }}">Sharing calendar in Microsoft Exchange</a></li>
 			<li><a href="{{ 'external/exchange-channels/asperaweb' | relative_url }}">AsperaWEB Quick Guide</a></li>
 			<li><a href="{{ 'external/exchange-channels/owncloud' | relative_url }}">Owncloud</a></li>
@@ -142,6 +143,7 @@ order: -1
 			<li><a href="{{ 'external/publication/publish-repo' | relative_url }}">Publish a repository</a></li>
 			<li><a href="{{ 'external/publication/add-gitignore' | relative_url }}">Add a .gitignore to your repository</a></li>
 			<li><a href="{{ 'external/publication/publishInBiotools' | relative_url }}">Publishing a tool in *bio.tools*</a></li>
+			<li><a href="{{ 'external/publication/phdThesisTemplate' | relative_url }}">LaTeX template for a doctoral thesis at University of Luxembourg</a></li>
 			<li><a href="{{ 'external/publication/10WaysImproveEnglish' | relative_url }}">10 ways to improve your English</a></li>
 		</ul>
 	</div>

external/exchange-channels/asperaweb/asperaweb.md

@@ -13,6 +13,8 @@ redirect_from:
 
 {:toc}
 
+> AsperaWEB will be deprecated in the future (the end of service is planned for January 2023). LCSB File Transfer (LFT) will be used instead ([LFT quick guide](https://howto.lcsb.uni.lu/?exchange-channels:lft)).
+
 ## Overview
 
 AsperaWEB is an IBM Aspera deployment at the LCSB-University of Luxembourg. AsperaWEB supports end-to-end encrypted data transfer and can handle high data volumes e.g. several tera bytes.
@@ -42,32 +44,27 @@ In the following steps we provide instructions on how to use AsperaWEB web inter
 2. When you visit a AsperaWEB access link for the very first time, you will be prompted to install or update **IBM Aspera Connect** client.
 
 * click **Download** or **Download the App** buttons (see below). <br/>![Alt](img/asperaweb_2.png "Title")
-
 * wait for the download to finish, the prompt should go to step 3. <br/>![Alt](img/asperaweb_3.png "Title")
-
 * open the installer just downloaded and start the installer. <br/>![Alt](img/asperaweb_4.png "Title")
-
 * close the installer, the Aspera Connect should try to open - *depending on your Operating System you may be asked if you are sure to open it* -
-
 * the prompt should disappear
-
 * restart your browser
 
-1. The **access link** page will display a **File Browser** section. Depending on the settings per access link, users can create or delete folders in the File Browser and upload and/or download data.<br/>
+3. The **access link** page will display a **File Browser** section. Depending on the settings per access link, users can create or delete folders in the File Browser and upload and/or download data.<br/>
   ![Alt](img/asperaweb_6.png "Title")
 
-2. Clicking **Upload** or **Download** will launch the **IBM Aspera Connect** client on your computer. You first will be asked whether you allow the client to connect to aspera.lcsb.uni.lu. Choose **Allow**.
+4. Clicking **Upload** or **Download** will launch the **IBM Aspera Connect** client on your computer. You first will be asked whether you allow the client to connect to aspera.lcsb.uni.lu. Choose **Allow**.
 
-3. At any time you can launch **IBM Aspera Connect** to display the status of uploads to or downloads from your computer. <br/>
+5. At any time you can launch **IBM Aspera Connect** to display the status of uploads to or downloads from your computer. <br/>
   ![Alt](img/asperaweb_8.png "Title")
 
-4. All data are encrypted on server side and they stay encrypted also upon download. For decryption, you have to navigate into your **IBM Aspera Connect** window and click "**Unlock encrypted files**". <br/>
+6. All data are encrypted on server side and they stay encrypted also upon download. For decryption, you have to navigate into your **IBM Aspera Connect** window and click "**Unlock encrypted files**". <br/>
   ![Alt](img/asperaweb_9.png "Title") <br/>
 You will be prompted for encryption passphrase which is present on the file browser. <br/>
   ![Alt](img/asperaweb_10.png "Title") <br/>
 Encrypted files are by default kept on your disc after decryption. If you want to change this behaviour, navigate to Options->Settings and check "Delete encrypted files when finished" box.
 
-5. You can also navigate to the help section on the top right of the browser. It contains information and links to get support.
+7. You can also navigate to the help section on the top right of the browser. It contains information and links to get support.
 
 <a name="ASPERAWEB_CLI"></a>
 
@@ -101,3 +98,11 @@ Specifically your firewall should:
 * If you have a local firewall on your server (like Windows Firewall), verify that it is not blocking your SSH and fasp transfer ports (e.g. TCP/UDP 33001).
 
 Detailed information on how to configure firewalls when working with Aspera is given [here](https://download.asperasoft.com/download/docs/p2p/3.5.1/p2p_admin_win/webhelp/dita/configuring_the_firewall.html).
+
+### Command-Line error "command not found: ascp" ###
+
+Run `ascli config ascp show` to show a path of `ascp`.
+
+Modify command with the path instead of `ascp`:<br>
+Here is an example of download command
+`<path-to-ascp-executable> -d -i $SSHKEY -P 33001 --file-crypt decrypt -W $TOKEN app_duma_private@aspera.lcsb.uni.lu:/<remote-dir> </local-dir>`

external/exchange-channels/lft/lft.md

+---
+card_order: 100
+layout: page
+permalink: /external/exchange-channels/lft/
+shortcut: exchange-channels:lft
+redirect_from:
+  - /cards/exchange-channels:lft
+  - /external/cards/exchange-channels:lft
+---
+# LCSB file transfer (LFT) Quick Guide
+
+{:toc}
+
+## Overview
+
+LCSB File Transfer (LFT) is a tool based on IBM Aspera software that supports end-to-end encrypted data transfer and can handle high data volumes e.g. several tera bytes.
+
+## Obtaining a LFT access link
+
+You need an **access link** to use LFT. An access link is a temporary, password-protected space, much like a drop box, on LCSB file transfer server. In order to obtain an access link, you should contact your research collaborator at the LCSB-University of Luxembourg. Once created, you will receive your **access link** and associated **password** by e-mail.
+
+> **IMPORTANT NOTE: Whenever the LCSB shares a password for an LFT endpoint (collaborator), the password is transmitted via a link which will expire in one week. Therefore you should make a record of your password once you view it.**
+
+An access link can be reached via standard web browsers. Data can be transferred to/from an access link in two ways:
+
+* Through the web browser by visiting the link, which is our recommended way of data transfer, described in this [section of the guide](#LFT_WEB).
+* Through the use of a command line tool. If your data sits in an environment, where you can not launch a web browser, then you may use a command line client tool to reach an access link. This process is described in this [section of this guide](#LFT_CLI).
+
+The use of LFT is mediated by LCSB's data stewards. If you require assistance in using LFT, you should send an email to the [LCSB datastewards](mailto:lcsb-datastewards@uni.lu) or refer to the [Troubleshooting](#LFT_TROUBLESHOOTING) section of this guide.
+
+<a name="LFT_WEB"></a>
+
+## Accessing LFT via Web Interface
+
+In the following steps we provide instructions on how to use LFT web interface.
+
+1. Once you receive your **access link** and **password** from the LCSB, visit the link using a standard web browser. Firefox 66.x (or higher) is recommended, but others should also work. You will be prompted for your password (see below).<br/><br>
+ ![Alt](img/lft_password.png "Password request")
+
+2. When you visit an LFT access link for the very first time, you will be prompted to install or update **IBM Aspera Connect** client.
+
+* click **Install Connect** button (see below). <br/>![Alt](img/lft_install.png "Install Aspera Connect")
+* open the installer just downloaded and start the installer. <br/>![Alt](img/lft_installAsperaConnect.png "Run installation of Aspera Connect")
+* close the installer - *depending on your Operating System the Aspera Connect can try to open and you may be asked if you are sure to open it* -
+* the prompt should disappear and you should see the following message <br/>![Alt](img/lft_AsperaConnectInstalled.png "Aspera Connect is installed")
+
+3. The **access link** page will display a **File Browser** section. Depending on the settings per access link, users can create or delete folders in the File Browser and upload and/or download data.
+
+  ![Alt](img/lft_fileBrowser.png "File Browser")
+
+4. Clicking **Upload** or **Download** icons will launch the **IBM Aspera Connect** client on your computer. You first will be asked whether you allow the client to connect to the server. Choose **Allow**.
+> Note: to download file/folder you need to select it first.
+
+5. At any time you can launch **IBM Aspera Connect** to display the status of uploads to or downloads from your computer. <br/>
+
+  ![Alt](img/lft_status.png "Aspera Connect status")
+
+6. All data are encrypted on server side and they stay encrypted also upon download. For decryption, you have to navigate into your **IBM Aspera Connect** window and click "**Unlock encrypted files**". <br/>
+
+  ![Alt](img/lft_AsperaConnect.png "IBM Aspera Connect") <br/>
+
+You will be prompted for encryption passphrase which is present on the file browser (click on the copy icon to copy into clipboard).
+
+  ![Alt](img/lft_encryptionPassword.png "Encryption password") <br/>
+  ![Alt](img/lft_AsperaCrypt.png "File decryption") <br/>
+Encrypted files are by default kept on your disc after decryption. If you want to change this behaviour, navigate to Options->Settings and check "Delete encrypted files when finished" box.
+
+7. You can also navigate to the help section on the top of the browser. It contains information and links to get support.
+
+<a name="LFT_CLI"></a>
+
+## Accessing LFT via Command-Line Tool
+
+In the following steps we provide instructions on how to use LFT command line.
+
+1. To access LFT via command line you need to have Aspera Connect be installed (see step 2 above).
+
+2. To transfer data you need to authenticate your connection. Authentication is done via SSH for which you need **SSH private key**. That key comes with the Aspera Connect installation and is named `aspera_tokenauth_id_rsa`. You need to know the location of SSH private key. Please see the table below for the list of locations depanding on your operational system:
+
+| Environment | Location | Alternate location |
+|-|-|-|
+| MacOS	| `$HOME/Applications/Aspera\ Connect.app/Contents/Resources/aspera_tokenauth_id_rsa` | `/Applications/Aspera\ Connect.app/Contents/Resources/aspera_tokenauth_id_rsa` |
+| Windows | `C:\\Program Files (x86)\Aspera\Aspera Connect\etc\aspera_tokenauth_id_rsa` |`C:\\Users\username\AppData\Local\Programs\Aspera\Aspera Connect\etc\aspera_tokenauth_id_rsa` |
+| Linux | `$HOME/.aspera/connect/etc/aspera_tokenauth_id_rsa` | `/opt/aspera/etc/aspera_tokenauth_id_rsa` |
+| Iris | `/opt/apps/resif/data/production/$PROD_VERSION/default/software/tools/Aspera-CLI/$CLI_VERSION/etc/aspera_tokenauth_id_rsa` | |
+
+3. Go to the help section of your access link.
+
+![Alt](img/lft_help.png "Help section") <br/>
+
+And follow instructions there. Export variables and execute the command to download/upload data.
+
+![Alt](img/lft_command.png "Help command line") <br/><br/>
+
+<a name="LFT_TROUBLESHOOTING"></a>
+## Troubleshooting
+
+You can use the official [IBM Aspera Diagnostic Tool](https://test-connect.asperasoft.com/) to troubleshoot your connectivity issues.
+
+### **Using Microsoft Edge browser**
+
+Microsoft Edge browser requires to download and install [IBM Aspera Connect for Edge](https://microsoftedge.microsoft.com/addons/detail/ibm-aspera-connect/kbffkbiljjejklcpnfmoiaehplhcifki).
+
+### **UDP/TCP port and firewall**
+
+> **IMPORTANT NOTE:** Aspera requires UDP ports to be enabled on firewalls.
+
+Specifically your firewall should:
+
+* Allow outbound connections from the Aspera client on the TCP port (TCP/33001, by default, when connecting to a Windows server, or on another non-default port for other server operating systems).
+* Allow outbound connections from the Aspera client on the fasp UDP port (33001, by default).
+* If you have a local firewall on your server (like Windows Firewall), verify that it is not blocking your SSH and fasp transfer ports (e.g. TCP/UDP 33001).
+
+Detailed information on how to configure firewalls when working with Aspera is given [here](https://download.asperasoft.com/download/docs/p2p/3.5.1/p2p_admin_win/webhelp/dita/configuring_the_firewall.html).
+
+### Command-Line error "command not found: ascp" ###
+
+Run `ascli config ascp show` to show path of `ascp`.
+
+Modify command with the path instead of `ascp`.
+
+Here is an example of download command
+
+`<path-to-ascp-executable> -d -i $SSHKEY -P 33001 --file-crypt decrypt -W $TOKEN $ASPERA_USERNAME@aspera-hts-01-srv.lcsb.uni.lu:/<remote-dir> </local-dir>`
\ No newline at end of file

external/publication/phdThesisTemplate/phdThesisTemplate.md

+---
+card_order: 850
+layout: page
+permalink: /external/publication/phdThesisTemplate/
+shortcut: publication:phdThesisTemplate
+redirect_from:
+  - /cards/publication:phdThesisTemplate
+  - /external/cards/publication:phdThesisTemplate
+---
+
+# LaTeX template for a doctoral thesis at University of Luxembourg
+
+A LaTeX template for PhD theses is available in GitLab at
+[outreach/templates/unilu-thesis-template](https://gitlab.lcsb.uni.lu/R3/outreach/templates/thesis).
+
+The repository includes several main items of interest:
+
+- In the `guidelines/` directory, there is a snapshot of the official
+  "Practical information for Prospective PhD candidates" PDF, which contains
+  some official recommendations regarding the thesis formatting.  The snapshot
+  is provided there only for convenience and its version is not necessarily
+  authoritative -- ask your supervisor and committee if there is a newer
+  version.
+
+- **The thesis template itself**, present mainly in files `thesis.tex` and
+  `macros.tex`. You are supposed to fill in your credentials into
+  `metadata.tex`, and then continue editing the other files (`summary.tex`,
+  `intro.tex`, ...) with the usual LaTeX thesis contents.
+
+- **A simple build system for producing a PDF with the typeset thesis**. If you
+  develop in GitLab or on GitHub, the thesis repository is configured so that
+  it will automatically run a CI and produce a PDF artifact with the thesis
+  whenever you push a new commit. To build the thesis yourself on your
+  computer, you should be able to do it using any standard, sufficiently recent
+  TeXlive distribution, or alternatively using Docker. The documentation in the
+  repository `README.md` contains several hints on how to do that.
+
+- The default thesis text (that you are supposed to erase and rewrite) contains
+  **some minor hints about the structure of the thesis** (mainly the headings
+  of the 4 main chapters), and various collected advice and demos on how to
+  nicely typeset the usual material that is found in the theses, such as
+  citations, figures, tables, mathematics, cross-references, appendices, etc.
+  Various other things (table of contents, section numbering, ...) work
+  automatically and correctly by default.
+
+The official requirements on the thesis formatting are, apart from the
+mandatory contents of the front page, committee member list and affidavit,
+mostly free-form. You are allowed to customize most of the thesis look to match
+the style and topic of your thesis and the requirements of your supervisor.
+
+In case you think the thesis template should be updated, please
+[open an issue in GitLab](https://gitlab.lcsb.uni.lu/R3/outreach/templates/thesis/-/issues/new)
+or send a merge request. Common concerns that substantiate opening an issue
+include the following:
+- Because the official recommendations and requirements on the thesis form may
+  change in the future, **in case you find any serious discrepancy between the
+  current recommendations and the thesis template, please let the template
+  maintiners know** by opening the issue, so that it can get corrected. If
+  possible, attach whatever document that summarizes the new guidelines.
+- If you require some specific LaTeX functionality that you think should be
+  present in the template (such as advanced indexes, lists of
+  floats/figures/tables, special typesetting and fonts, ...).
+- If you want to share a hard-learned truth or a good approach to solve
+  common problems with other students.