10/18/2020 How To Download Qiime Mac
Warning
The following steps require at least ~25 GB of free disk space: ~5 GB for the ZIP file, ~5 GB for the unzipped ZIP file contents, and ~15 GB for the installed Virtual Machine (VM). Once you have installed the VM you can free up ~10 GB of space by deleting the ZIP + the unzipped ZIP file contents.
The QIIME 2 VirtualBox image offers a convenient way to get QIIME 2 up and running, and is also the easiest way to get your hands on the experimental preview of QIIME 2 Studio.
1. Install VirtualBox on your computer¶
Please see https://www.virtualbox.org for details on how to install VirtualBox on your computer. Please note, some computers require activating a BIOS setting to enable virtualization — please consult your hardware documentation to determine if you need to do this, and how. After installing VirtualBox, take note of the version of VirtualBox that was installed.
2. Download the QIIME 2 Core VirtualBox Image¶
Please note, this installation document uses some placeholders throughout the following steps.
X.Y.Z represents the version of QIIME 2 (e.g. 2020.8 ), and build_number represents the build identifier for the VirtualBox image (an internal reference used by the QIIME 2 Developement Team). Please see the VirtualBox Images download link to get the download URL for the latest image. The minimum version of VirtualBox (as determined in Step 1 above) is provided for the latest releases of the VirtualBox image — please ensure you have installed a version of VirtualBox that is equal to or greater than the version of the QIIME 2 VirtualBox image you wish to install.
Analyzing FASTQ Files Using QIIME Overview Once DNA has been sequenced, the sequencer will output information in the form of a FASTQ file. These files are run through a series of scripts to extract data from the files. The scripts are part of a free data analysis package offered by QIIME (Quantitative Insights Into Microbial Ecology qiime.org). Apr 18, 2020. Metadata Formatting Requirements¶. QIIME 2 metadata is most commonly stored in a TSV (i.e. Tab-separated values) file. These files typically have a.tsv or.txt file extension, though it doesn’t matter to QIIME 2 what file extension is used. TSV files are simple text files used to store tabular data, and the format is supported by many types of software, such as editing, importing,.
3. Unzip the file¶
Unzip/extract the
qiimeX_Y_Z-build_number.zip file and open the directory that you chose to unzip to. Please note, some operating systems (e.g. Windows) open a read-only view of the ZIP file, which has not actually been extracted. Please follow the directions for your operating system/unarchiver tool as necessary.
4. Launch VirtualBox¶
Double-click the file named
QIIME2Core-X.Y.Z(build_number).ovf . Backyard baseball 2005 mac download.
Note
The file ending with the extension
ovf is a type of VirtualBox “recipe” — it allows the QIIME 2 developers to define a set of reasonable default configuration values, rather than requiring you to manually specify RAM, CPU count, etc. The file ending with the extension vmdk is the actual virtual machine disk image. If you don’t want to import using the defaults specified in the ovf you can use the vmdk file to manually import the VM — see the VirtualBox Docs for details.
You will be presented with an
ApplianceSettings import page. We have selected default settings for you that should work for most light workloads. If you are interested in changing the allocations (e.g. memory or CPUs), feel free to adjust these settings. When done, click Import .
Once the import is complete, double-click on the new Virtual Machine entry that matches the
X.Y.Z & build_number version that you just imported.
5. Launch the virtual machine¶
When prompted, select the user
qiime2 , and enter the password qiime2 .
Once logged in you should see a screen like this:
Success! To confirm that everything is working, you can open up a terminal and run the following command:
Note, the list of installed plugins (and their versions) will likely differ depending on the version of the VirtualBox virtual machine that you chose to download and install.
6. Clean up¶
The import process creates a copy of the files from the directory that you unzipped in step 3 above. If you would like to reclaim that disk space, feel free to delete
qiimeX_Y_Z-build_number.zip , and the unzipped folder from that file.
Optional: Shared Folders and Copy-and-Paste¶1. Install Guest Additions¶
Note
Optional: Guest Additions are already installed in the virtual machine, but if you need to reinstall (or update) them, you can perform the following steps.
Attach the Guest Additions DVD by following the instructions outlined in the VirtualBox Guest Additions Docs.
Once inserted, the Guest Additions DVD should automatically launch (if not, double-click the DVD and click the ‘Run Software’ button in the upper right:
Enter the password (
qiime2 ) when prompted.
When installation is done, your screen should look like the following. Follow the prompt and press
Return .
2. Set up copy-and-paste¶
In the VirtualBox menu bar on your host computer, select
Machine->Settings , then click General in the top bar, and Advanced in the bar immediately below it. We recommend setting SharedClipboard and Drag'n'Drop to Bidirectional , which will allow copy-and-paste from host-to-guest and from guest-to-host. The Drag'n'Drop allows you to drag folders into the window to copy them into your Virtual Machine. Click OK when you are done.
3. Set up a shared folder¶
In the VirtualBox menu bar on your host computer, select
Devices->SharedFolders->SharedFoldersSettings (note, this might be slightly different on Windows or Linux systems, please check the official VirtualBox Docs). Click on the green plus sign/folder on the right side of the window, you should see a new screen prompting you for info:
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Click on the
FolderPath input, and using the file browser (by selecting the option Other.. ), select the folder you want to share with the VM. This example uses the Desktop (e.g. /Users/matthew/Desktop on a Mac). Make sure to select Auto-mount and MakePermanent , if you don’t want to repeat these steps every time you launch the VM. Also note, the FolderName option (which VirtualBox will auto-suggest a value for) is the name of the mounted folder inside of your VM. VirtualBox will always prepend the prefix sf_ to that value (sf stands for sharedfolder ). So in this case, the folder name will be sf_Desktop . The full path when mounted is /media/sf_Desktop .
Click ‘OK’ on both dialogs to save your changes.
4. Reboot¶
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5. Enjoy!¶
Once the VM has rebooted and you have logged in, you should see your shared folder in the file browser (the icon on the left bar that looks like a file cabinet):
The files there are the files on the Mac’s desktop! These files can also access the mounted folder via the Command Line at
/media/sf_Desktop :
Lastly, if you want to create a symbolic link to your shared folder to a more convenient location on your VM, you can run the following command:
Where
sf_Desktop is the name of the shared directory from step 2 above, and ~/Desktop/shared is a location of your choosing.
This post introduces how to install Miniconda on Mac.
(For installing Miniconda on Linux OS, check out this post.)
(For commonly used conda commands check this post.)
(For the comparison among Anaconda, Miniconda, and Virtualenv with pip, check this post.)
Step 1: download Miniconda (bash installer) from
see the highlighted in the pic below.
A file called Miniconda3-latest-MacOSX-x86_64.sh will be shown in your Downloads folder.
Step 2: Open a Terminalwindow.
(If you don’t know how to open a terminal window, through lauchpad type in Terminal, you will see the application.)
In the terminal window, type in
Step 3: run the bash “shell” script to install Miniconda
In the terminal window, type in the following.
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Scroll through the license (press the Space bar or Enter to move through quickly), type ‘yes’ to approve the terms, and then accept all the installation defaults.
Step 4: Close the Terminal window, and open a new Terminal window.
in the newly opened Terminal window.
Type the following:
If you see something like the following, it means you have successfully installed conda via miniconda on your Mac.
conda 4.5.11
Step 5: Uninstalling Miniconda
To uninstall Python Anconda/Miniconda, we just simply remove the installation folder and remove the environment variables set in the hidden file .bash_profile in your home directory. For my installation, it will be just like this.
Then, you can edit the .bash_profile file and remove the following entries added for Anaconda/Miniconda directory from your PATH environment variable.
If you do not know where the hidden .bash_profile is located and how to edit it, see below for detailed instructions.
(1) Open a new terminal and go to your home directory. You can do this by using the command below.
(2) use the following command to list all files, including hidden files in your home directory.
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(3) Use the
cat command to see the contents of the hidden file .bash_profile. Type the following command into your terminal.
You will see something like the following (depends on what you installed, if you installed Miniconda3, you will only see the first two lines. If you installed Anaconda3, you will see the bottom two lines.
(4) To remove installed Miniconda/Anaconda from your .bash_profile use the command below to edit the file using the nano editor.
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Remove the Miniconda /Anoconda path in your .bash_profile hidden file.
Then Type control + X to exit out of nano
Save changes by typing Y.
Close the terminal, and now Miniconda/Anaconda should be successfully uninstalled from your Mac.
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(Tested on macOS Mojave. Note that you can install Miniconda onto your Mac even when you are not an admin user.)
For commonly used conda commands check this post.
For the comparison among Anaconda, Miniconda, and Virtualenv with pip, check this post.
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