diff --git a/Download_Installation.qmd b/Download_Installation.qmd index 9a58030..f45492e 100644 --- a/Download_Installation.qmd +++ b/Download_Installation.qmd @@ -1,9 +1,9 @@ --- title: "Download & Installation" author: "Cox Lab" -execute: +execute: eval: false -format: +format: html: toc: true toc-depth: 4 @@ -18,238 +18,169 @@ csl: nature.csl # Download -Downloading and using the software is free of charge. - -Simply download from [here](https://maxquant.org/) and unpack the compressed file `MaxQuant.zip`. +Downloading and using the software is free of charge. +Simply download from [MaxQuant.org](https://maxquant.org/) and unpack the compressed file `MaxQuant.zip`. # Running -Please choose your operating system to view how to run MaxQuant. +Choose your operating system to see how to run MaxQuant. -## MaxQuant on Windows {#sec-mq-windows} +**Supported Operating Systems (64-bit):** -Supported operation system versions (64-bit is required) are Windows 10 or 11 or Windows Server 2016, 2019, 2022. +- Windows 10 +- Windows 11 +- Windows Server 2016–2025 +- Ubuntu 20.04 or newer -- **Install .NET Core 8.0 or higher**: To find out whether you already have it, you can either open the following path. We recommend using version 8.0.302 at least, as it solves some bugs with the GUI. +## MaxQuant on Windows {#sec-mq-windows} -``` bash -C:\Program Files\dotnet\sdk -``` +**Install .NET Desktop Runtime 8.0** -or run the following command in the terminal (Win+R -\> `cmd`): +Check if it's already installed (Win+R -\> `cmd`): -``` bash -dotnet --version +```bash +dotnet --list-runtimes ``` -If you need to, you can download the software and get installation instructions e.g. [for .NET 8.0 here](https://dotnet.microsoft.com/en-us/download/dotnet/8.0). +If you need to install or update .NET, follow the instructions provided by [Microsoft for .NET 8.0](https://dotnet.microsoft.com/en-us/download/dotnet/8.0). -~~.NET 3.1 and older versions are not supported anymore.~~ +MaxQuant requires .NET >= 8.0.302. -MaxQuant now works with .NET \>= 8.0.302 +**Running MaxQuant** -- **Run MaxQuant GUI** Double click on `MaxQuant.exe` in the `MaxQuant` folder and specify your RAW files, experimental design and fasta files. - -- **Start MaxQuant** Click on the `Start` button. +- **GUI Mode:** Double-click `MaxQuant.exe` inside the `MaxQuant` folder. Specify your RAW files, experimental design, and FASTA files. +- **Start Analysis:** Click the `Start` button. ## MaxQuant on Linux -We are supporting MaxQuant on Ubuntu 20.04 or higher, but MaxQuant should also work on other distributions of Linux. -~~You may run MaxQuant using Graphical User Interface~~. MaxQuant on Linux doesn't support the use of a GUI at the moment. We're planning to make it available in future versions, [so stay tuned to our newletter](https://maxquant.org/newsletter/), where we'll inform our users about new updates. +MaxQuant is supported on Ubuntu 20.04 or newer, but it should also work on other distributions. Currently, MaxQuant on Linux does **not** have a GUI; only command-line usage is supported. A GUI may be offered in future releases. [Subscribe to our newsletter](https://maxquant.org/newsletter/) for updates. -This tutorial is focused on running MaxQuant using the command-line. +This tutorial focuses on command-line usage. -- **Install .NET Core 8.0** To find out whether you already have it, type in the command line +**Install .NET Runtime 8.0** -``` bash -dotnet --version -``` +Check if .NET 8.0 is installed: -If you see at least version $8.0.302$, then everything is ready to start MaxQuant. +```bash +dotnet --list-runtimes +``` -Otherwise you need to follow the installation instructions at [.NET Core SDK 8.0](https://dotnet.microsoft.com/en-us/download/dotnet/8.0) for your operating system. +If you see version `8.0.302` or newer, you're all set. Otherwise, follow the [official .NET installation instructions](https://learn.microsoft.com/en-us/dotnet/core/install/linux?WT.mc_id=dotnet-35129-website) for your distribution. -### Global installation on Ubuntu using `sudo` permissions +### Global Installation on Ubuntu (with `sudo` privileges) -Ubuntu 22.04 (for example) +For example, on Ubuntu 22.04: -``` bash -wget https://packages.microsoft.com/config/ubuntu/20.04/packages-microsoft-prod.deb -O packages-microsoft-prod.deb -sudo dpkg -i packages-microsoft-prod.deb -sudo apt-get update; \ -sudo apt-get install -y apt-transport-https && \ +```bash sudo apt-get update && \ -sudo apt-get install -y dotnet-sdk-8.0 +sudo apt-get install -y dotnet-runtime-8.0 ``` -### local installation using the `conda` environment +### Local Installation using `conda` (No `sudo` required) -An alternative installation method, which might work better, if no `sudo` rights are available for the user would be to use the `conda` [@anaconda] environment. +If you lack `sudo` privileges, you can install .NET via `conda` [@anaconda]. -Depending on your architecture, the user must choose between the x86 and the Arm installation scripts. -Both can be downloaded from the [anaconda repository](https://repo.anaconda.com/miniconda/) using the `wget` command. +1. **Download and Install Conda:** + ```bash + # Get the installer + mkdir -p ~/miniconda3 + wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-$(arch).sh -O ~/miniconda3/miniconda.sh -``` bash -# Or use conda to install an environment -## get the installer -mkdir -p ~/miniconda3 -# for 64x-bit 86x architecture -wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda3/miniconda.sh -# for 64-bit arm architecture -wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-aarch64.sh -O ~/miniconda3/miniconda.sh + # Install Conda + bash ~/miniconda3/miniconda.sh -b -u -p ~/miniconda3 + rm ~/miniconda3/miniconda.sh + ``` -### You'll only need one the above two scripts!!! +2. **Initialize Conda in Your Shell:** + ```bash + ~/miniconda3/bin/conda init bash + source ~/.bashrc + ``` -# Install the conda base env -bash ~/miniconda3/miniconda.sh -b -u -p ~/miniconda3 -rm -rf ~/miniconda3/miniconda.sh -``` - -Before one can use the `conda` environment in your shell, it must be initialized and the session restarted. -Another tip would be to install the mamba package, but **this is only optional** and is not needed, if you're using conda on a regular basis. -(If you do, you probably already installed mamba 😀). - -``` bash -# initialize conda on bash -~/miniconda3/bin/conda init bash -~/miniconda3/bin/conda init zsh -# logging out and back in again -conda install conda-forge::mamba -mamba init -#Here again, one must log out and back in again for mamba to be active. -``` +3. **Create a Conda Environment with .NET:** + ```bash + conda create -y -n dotnet8 conda-forge::dotnet-runtime=8 + conda activate dotnet8 + ``` -Now, using the `mamba`command one can create a new environment for `dotnet`. -One can either choose a specific version for `dotnet` or by omitting the version number, the latest available version on the anaconda repository will be installed. -You can search [here](https://anaconda.org/search?q=dotnet) for possible versions. - -Before you can use the tool, you must activate the environment. -Last check to see if the installation was successful, one can check for the available `dotnet` version. - -``` bash -#Now we create `dotnet` env -# create the dotnet env -mamba create -n dotnet8 conda-forge::dotnet=8.0.302 -mamba activate dotnet8 -#To test that we do have `dotnet` -dotnet --version -``` +### Scripted Installation Using Microsoft Resources -### Scripted installation using Microsoft resources. +You can also install .NET using the official Microsoft `dotnet-install` script: -One can also follows Microsoft's instruction to install the (optional) latest version of`.NET` by following the script [here](https://dotnet.microsoft.com/en-us/download/dotnet/8.0). - -A manual install has more options to choose from using the `dotnet-install` script from the [.NET page](https://learn.microsoft.com/en-us/dotnet/core/tools/dotnet-install-script). - -``` bash +```bash wget https://dot.net/v1/dotnet-install.sh -O dotnet-install.sh chmod +x ./dotnet-install.sh -./dotnet-install.sh --channel 8.0 +./dotnet-install.sh --channel 8.0 --runtime dotnet ``` -Possible important options here are: +**Important options:** -- `--channel` - use this to ask for a specific version and/or subversion -- `--version` - install a specific version -- `--install-dir` - use this to specify the path to the installation directory. +- `--channel`: Specify a .NET channel or version (e.g., `8.0`). +- `--version`: Install a specific version. +- `--install-dir`: Specify the installation directory. -We also added a script for an automated installation of the .NET which can also be downloaded [here](Install_dotnet.sh). -Running the script will ask the user for a download location, where, for now, .NET version 8.0.302 will be installed. -This version was needed due to a bug in Perseus. +We also provide a helper script [Install_dotnet.sh](Install_dotnet.sh) for automated installation of .NET 8.0.302. This version was chosen due to a bug in Perseus requiring that version. -After downloading the script it needs to be made executable and can be run as such: +After downloading `Install_dotnet.sh`, make it executable and run it: -``` bash -chmod -x Install_dotnet.sh +```bash +chmod +x Install_dotnet.sh sh Install_dotnet.sh INSTALLATION_PATH/ ``` -This will download the .NET installation script from Microsoft and will install the tool at the given path. -no `sudo` rights are needed. +This will install .NET at the specified path without requiring `sudo` privileges. -## Edit mqpar.xml file +## Editing the `mqpar.xml` File -Currently we highly recommend to pre-configure the `mqpar.xml` file in MaxQuant GUI. After transferring the file on Linux machine, do not forget to update file addresses accordingly. -You can also use a programmatic way to change that. +We recommend pre-configuring the `mqpar.xml` file using the MaxQuant GUI on Windows. After transferring it to a Linux machine, update the file paths accordingly. You can also update paths programmatically. -If you use on-the fly prediction use this command: +- **If using on-the-fly prediction:** + ```bash + dotnet MaxQuant/bin/MaxQuantCmd.dll old_mqpar.xml --changeFolder new_mqpar.xml + ``` -If you use on-the-fly prediction use this command: +- **If using predicted libraries:** + ```bash + dotnet MaxQuant/bin/MaxQuantCmd.dll old_mqpar.xml --changeFolder new_mqpar.xml + ``` -``` bash -dotnet MaxQuant/bin/MaxQuantCmd.dll old_mqpar.xml --changeFolder new_mqpar.xml +If you are familiar with `mqpar.xml` structure, you can create and edit a template directly: +```bash +dotnet MaxQuant/bin/MaxQuantCmd.dll --create new_mqpar.xml ``` -<<<<<<< Updated upstream -If you use predicted libraries, you need to also add the path to the saved libraries, so use this command: -======= -If you use predicted libraries, you also need to add the path to the saved libraries, so use this command: ->>>>>>> Stashed changes +## Running MaxQuant -``` bash -dotnet MaxQuant/bin/MaxQuantCmd.dll old_mqpar.xml --changeFolder new_mqpar.xml +Once everything is set up: +```bash +dotnet MaxQuant/bin/MaxQuantCmd.dll mqpar.xml ``` -However if you feel familiar with a structure of `mqpar.xml`, you may create a template of `mqpar.xml` and edit it directly. +# Hardware Requirements -``` bash -dotnet MaxQuant/bin/MaxQuantCmd.dll --create new_mqpar.xml -``` +### Minimum Entry-Level Configuration +- x86_64 CPU +- At least 8 GB of RAM +- Add 4 GB of RAM for each additional MaxQuant processing thread -## Run MaxQuant +### Recommended Standard Configuration +- Modern Intel Core or AMD Ryzen CPU +- 64 GB RAM +- 2 TB NVMe SSD (or larger) -``` bash -dotnet MaxQuant/bin/MaxQuantCmd.dll mqpar.xml -``` +## Real-World Examples + +### Single-User Workstation +- CPU: AMD Ryzen 9 9950X (16 cores) +- Memory: 96 GB DDR5-6000 (2x 48 GB) +- Storage: WD_BLACK SN850X NVMe SSD 4TB + +### Small Multi-User Server +- CPU: AMD Epyc 9334 (32 cores) +- Memory: 384 GB DDR5-4800 (12x 32 GB) +- OS/Software Storage: Samsung PM9A3 NVMe SSD 1.92 TB (2x in HW-RAID1) +- Temporary Data Storage: Solidigm D5-P5336 NVMe SSD 15.36TB (2x in SW-RAID1) + +--- -# Hardware requirements - -- 4 GB RAM minimum. -- 4 GB RAM per thread that is executed in parallel is required. -- There is no upper limit on the number of cores. Whatever you can fit into a shared memory machine will work as long as the disk performance scales up with it. - -Here we list some example hardware configurations that we are using in the lab and that we are quite happy with. -These are mere examples and there is no reason to prefer specific vendors or brands. - -### Dell PowerEdge R820 (Intel) - -- 4x Intel® Xeon® E5-4640 2.40GHz, 20M Cache, 8.0GT/s QPI, Turbo, 8C, 95W -- 128GB Memory for 4CPU (16x8GB RDIMM, 1600 MHz, Standard Volt, Dual Rank, x4) -- PERC H710p integrated RAID Controller, 1GB NV Cache -- 6x 900GB, SAS 6Gbps, 2.5-in, 10K RPM Hard Drive (Hot Plug) -- RAID-0 -- OS: Microsoft Windows Server 2012 Standard - -### Standard PC - -- Processor: Intel® Core i7-2600 Processor (8M Cache,3.40 GHz) -- OS: English original Windows® 7 Professional(64-Bit) -- RAM: 16GB (4X4GB) 1333 MHz DDR3 Non-ECC 489916 1 \[370-20205\] 3 -- Primary Hard Drive: 256GB SSD Solid State Drive -- Additional Hard Drive: 2TB (7.2k rpm) Serial ATA II with NCQ and 16MB Data Burst Cache -- Graphics card: 512MB AMD Radeon HD 6350 -- USB 3.0: USB 3.0 PCI-Card -- To improve the processing speed the SSD can also be used exclusively for MaxQuant -- USB 3.0 convenient for fast file transfer, 500MByte/s (USB 2.0 = 60MByte/s) -- Hard drives can of course be larger depending on the respective sizes of your projects and wallet. - -### 'Monster' PC - -- Coolermaster HAF 922 Black Tower Case -- 2 x Front USB 2.0 and Audio ports -- 750W EPS12V Quiet power supply -- Additional Red LED 200mm Case Fans -- Asus Sabertooth P67 Intel i7 Skt1155ATX motherboard With 2 x 16x 2.0 PCI-Express slot, 3 x PCI-e x1 slot, SATAIII 4 x DDR3 memory slots, Audio, 10/100/1000 LAN, SATAII, & USB 3.0/USB 2.0 ports -- Intel i7 2600K 3.4GHz Quad Core 8MB cache Skt1155 Unlocked processor -- Corsair Vengeance 32GB (4 x 8GB) DDR3 1866MHz Quad Channel memory -- Western Digital 500GB Caviar Black SATAIII disk drive -- 1GB Nvidia Geforce GT430 PCI-e x16 2.0 graphics card -- Black DVD+/- R RW Dual Layer drive -- LSI 9260-8i 8port SAS 6Gb/s PCI-Express RAID controller -- Battery Backup for RAID controller -- 2 x Crucial 512MB Solid State Disks -- Thanks to Peter McHardy for assembling this configuration - ------------------------------------------------------------------------- - -For questions or problems with the installation we would love to hear from you under [Contact](contact.html). +If you have questions or encounter problems with the installation, please [contact us](contact.html). \ No newline at end of file diff --git a/docs/Download_Installation.html b/docs/Download_Installation.html index e539f9f..b839ba1 100644 --- a/docs/Download_Installation.html +++ b/docs/Download_Installation.html @@ -7,7 +7,7 @@ - + Download & Installation