From 1354735f17aa764f882796552937c8ed8ac80c40 Mon Sep 17 00:00:00 2001 From: richelbilderbeek Date: Tue, 14 May 2024 07:47:33 +0200 Subject: [PATCH] docs/cluster_guides/transit.md is a short page --- docs/cluster_guides/software_on_transit.md | 41 ++++++++++++++++++ docs/cluster_guides/transit.md | 49 +++------------------- 2 files changed, 46 insertions(+), 44 deletions(-) create mode 100644 docs/cluster_guides/software_on_transit.md diff --git a/docs/cluster_guides/software_on_transit.md b/docs/cluster_guides/software_on_transit.md new file mode 100644 index 000000000..3f724e9d1 --- /dev/null +++ b/docs/cluster_guides/software_on_transit.md @@ -0,0 +1,41 @@ +# Software on Transit + +[Transit](../cluster_guides/transit.md) +is an UPPMAX service that can be used to securely transfer files. + +This page describes the software on [Transit](../cluster_guides/transit.md). + +After [logging in to Transit](../cluster_guides/login_transit.md), +you cannot make lasting changes to anything, +except for mounted [wharf](../cluster_guides/wharf.md) directories. +However, anything you have added to your [Rackham](../cluster_guides/rackham.md) home directory +is available on [Transit](../cluster_guides/transit.md). + +In addition, some modules are available. + + * SciLifeLab Data Delivery System - [https://delivery.scilifelab.se/](https://delivery.scilifelab.se/) + + ```bash + # Load the tool from the software module tree + module load bioinfo-tools dds-cli + + # Run the tool + dds + ``` + ![dds-cli](../img/dds-cli.png) + +To download data from TCGA, +[log in to Rackham](../getting_started/login_rackham.md) +and install the GDC client to your home directory. +Then [logg in to Transit](../cluster_guides/login_transit.md), +mount the [wharf](../cluster_guides/wharf.md), +and run `./gdc-client`. + +!!! warning "2FA on transit" + + If you connect from abroad and + you are asked for the **2FA** (_two factor authentication_), + there is a grace period (_about 5 minutes_) in which you can + `ssh`/`scp`/`rsync`/`sftp` to **transit** without the need for **2FA**. + This allows you to use these and other tools + that might experience problems with the **2FA**. diff --git a/docs/cluster_guides/transit.md b/docs/cluster_guides/transit.md index 35eb0e939..68aab947e 100644 --- a/docs/cluster_guides/transit.md +++ b/docs/cluster_guides/transit.md @@ -1,6 +1,7 @@ # Transit -Transit is an UPPMAX service that can be used to securely transfer files. +[Transit](../cluster_guides/transit.md) +is an UPPMAX service that can be used to securely transfer files. ???- question "Is Transit a file server?" @@ -30,46 +31,6 @@ Transit is an UPPMAX service that can be used to securely transfer files. Here, 'putting an address on the letter' is to copy the file to the desired location. -This page shows: - -- [how to log in to Transit](#log-in-to-transit) -- [software on Transit](#software-on-transit) -- [file transfer using Transit](transfer_transit.md). - -## Log in to Transit - -See [log in to Transit](../cluster_guides/login_transit.md). - -## Software on Transit - -After [logging in to Transit](../cluster_guides/login_transit.md), -you cannot make lasting changes to anything, -except for mounted wharf directories. -However, anything you have added to your Rackham home directory -is available on Transit. - -In addition, some modules are available. - - * SciLifeLab Data Delivery System - [https://delivery.scilifelab.se/](https://delivery.scilifelab.se/) - - ```bash - # Load the tool from the software module tree - module load bioinfo-tools dds-cli - - # Run the tool - dds - ``` - ![dds-cli](../img/dds-cli.png) - -To download data from TCGA, -log in to Rackham and install the GDC client to your home directory. -Then log in to Transit, mount the wharf, and run ./gdc-client. - -!!! warning "2FA on transit" - - If you connect from abroad and - you are asked for the **2FA** (_two factor authentication_), - there is a grace period (_about 5 minutes_) in which you can - `ssh`/`scp`/`rsync`/`sftp` to **transit** without the need for **2FA**. - This allows you to use these and other tools - that might experience problems with the **2FA**. + * [how to log in to Transit](../cluster_guides/login_transit.md) + * [file transfer using Transit](../cluster_guides/transfer_transit.md). + * [software on Transit](../cluster_guides/software_on_transit.md)