Bioinformatics Software For Mac

“ExPASy is the SIB Bioinformatics Resource Portal which provides access to scientific databases and software tools (i.e., resources) in different areas of life sciences including proteomics, genomics, phylogeny, systems biology, population genetics, transcriptomics etc”. Lists of Genomics Software/Service Providers This list is intended to be a comprehensive directory of genomics software, genomics-related services and related resources. Some collaborators and I are also working on a more usable and complete resource at.

♦ 2.2k wrote: I have no experience with them, but there are several Linux distributions out there that come preloaded with bioinformatics software. ♦ 7.3k wrote: All of the 3 major platforms have their advantages, and I use all 3 practically every day. Mac OS X is my primary desktop OS, for a number of reasons, but mostly because I just seem more productive using it than any of the alternatives. All of my coding work is done over SSH on Linux (almost exclusively Ubuntu) servers. The power of Aptitude package management, and the robustness of this platform means that there really is no other choice for this kind of work. Finally I run Windows 7 on my netbook, because it is an excellent OS for that platform, and enables me to do everything I want that machine to be capable of, note-taking, blog writing, as a display machine for Powerpoint etc.

It is also useful to have Internet Explorer kicking around somewhere for compatability testing. I wouldn't consider using any machine that I didn't have admin rights on for work purposes, if I have to jump through hoops to get stuff installed, it just slows me down too much. This is another reason for using OS X for my primary desktop, it allows me to escape the University's 'Common Desktop' policy for Windows PCs, which would take control of my computer out of my hands. 40 wrote: I have a Mac Pro dual quad core that I use for everything. I use the Mac OS for day to day email, most graphics, browsing, I run a VMWare virtual Windows machine, and I do most analysis in the unix terminal. Windows runs much better on the Mac hardware, Excel is much faster in Window, and I can fileshare between the Windows and Mac systems.

So far this has been sufficient for me. If I run into a situation where I need more computing power, I can ssh to a Linux server, but I haven't needed to yet. I configured the machine with 16 GB RAM, leaving slots open to add another 16 if needed. I've been happy with this. ♦♦ 78k wrote: Often people are limited to their choices by factors outside of their control.

One lab that I work with requires the use of Mac computers another is using Windows mostly. Large scale computations seem to be best suited for Linux systems. Luckily there is a migration towards unified capabilities across all platforms. Installing Cygwin on Windows allows us to tap into the power of Unix, while Linux distros have advanced graphical user interfaces like Windows and Macs. From my own observations of non technical people, the installation of new and interdependent software packages seems to be the most difficult on Mac computers and easiest on Windows due to the computational architecture that makes all Windows computers identical.

2.7k wrote: Most stuff we do is done on a linux HPC that runs CentOS. People access this in different ways, but my preffered set up is a big windows box (Xeon, 32GB RAM) running a Xubuntu VM (which gets 20GB of that RAM). I have SSHFS pipes set up to the disk areas on the HPC that allows me edit code in local editors, and a terminal with SSH to the cluster to run things. There is no real reason that I couldn't do this in Windows, particularly with WSL, although getting sshfs working on windows has always seem a bit of a pain. It would also probably work just as well on Mac, though I guess a Mac box that big would set me back significantly more than the windows box did (around £800). Occasionally I want to run local RStudio or Juptyer (operating on files over SSHFS), and I find that works better on Linux than windows. We don't have root access on the cluster, and that has occasionally been an annoyance, but to be honest conda and bioconda has eased almost all that pain, and where things arn't available in conda, I've yet to come accross something that can't be complied from source without admin rights with a little bit of effort.

Information Technical Specs Support Pathway Tools Installation Guide - Linux and MacOS X (Intel only) Pathway Tools Installation Guide - Linux and MacOS X (Intel only) The following instructions are for the supported UNIX systems, namely modern flavors of Linux x86, Linux x8664, and MacOS X 10.8+ (Intel only). Contents. Pathway Tools is known to run on MacOS X 10.4 and higher, Intel only. Pathway Tools requires that X11 be installed.

In all recent versions of MacOS (10.6+), it should be installed by default. You can check if you have X11 installed by clicking on the Finder menu Go-Utilities. You should see an entry for XQuartz, which is Apple's version of X11.

For MacOS 10.13 (High Sierra) and later, you may see a pop-up saying the software is 'not optimized' for MacOS. It is OK to click through this; we will fix this in a later release. When running the uninstaller, the dialog that starts it up may pop up.behind.

the main dialog box. You will have to click on it to raise it. We expect that in the next release the installer software will be much more Mac-friendly. Decide where to install Pathway Tools. For a single user, your home directory is strongly recommended.

This is the default location suggested by the installer. Download the Pathway Tools distribution file. Safari users note: You must download the file with Control-Mouseclick, and select 'Download Linked File' from the popup. These files are of the form pathway-tools-version-platform-edition-install.dmg where version is 15.0 for this release, platform is 'macosx', and edition could be 'collaborator', 'tier1' and so on.

An example would be pathway-tools-15.0-macosx-tier1-install.dmg The URLs pointing to these distributions can be found in the confirmation email that is sent after signing the license agreement. Please retain this email, as the same URLs will be used for every new release. Please also ensure that the correct distribution is selected for your specific platform.

The.dmg files are disk images that can be mounted by double-clicking on them. A Finder window should appear which contains the actual installer. Double-click the installer file. A GUI-based installer will guide you through the rest of the installation process. The installer will suggest you close all applications before continuing and give you the opportunity to cancel the installation. Click Next.

The installer will ask you where you want to install the Pathway Tools system. If you are running as a normal user, it will suggest a location in your home directory. If you are installing as the root user, it will suggest /usr/local/pathway-tools as a location. The latter is convenient if many users will be using Pathway Tools.

Click Next once you have chosen a suitable location. Pathway Tools requires a directory where it will store local user data such as created PGDBs and HTML customization files. The installer will ask you to specify a directory path where Pathway Tools can create this 'ptools-local' directory. Please make sure that all users who will update PGDBs have write permission to the ptools-local directory and its subdirectories.

The default directory is the home directory of whoever is running the installer, which means that the data will reside in a directory called /ptools-local. IMPORTANT NOTE Do not install the ptools-local directory under your Pathway Tools installation directory, since the data in this directory would then be deleted when Pathway Tools is upgraded or reinstalled.

Click Next once you have chosen a suitable location. The system will pop up a dialog describing the installation. If the information it gives is not suitable, you can click the Back button to revisit previous dialogs. Click Next to do the actual installation. If you already have Pathway Tools installed, the installer will pop up a dialog asking if it can uninstall this previous installation.

We highly recommend that you allow the installer to uninstall the previous version. Incorrect operation may result if the previous version is not uninstalled before installing the new version. Unless you are installing this versionof Pathway Tools in a different place, choose Yes from this dialog to uninstall the previous version. The uninstaller for the previous version will then pop up a dialog asking for permission to uninstall the previous version.

Answer Yes to continue.Warning!. The uninstaller dialog for the old Pathway Tools may pop up.behind. the installer window with just the edges visible. Please click on it to bring it to the front. Once the files are installed, the installer will pop up a pane reminding you of the location of the ptools-local directory.

After a successful installation of Pathway Tools, a file with initialization parameters will have been written in this directory, retaining values from a prior installation if possible. The resulting file can be found in ptools-local/ptools-init.dat. This file may be customized and edited to define additional parameters specific to your site. Please see the Pathway Tools User Guide for more details on how to customize the ptools-init.dat file. Click Finish to finish installing Pathway Tools. The installer will then pop up a banner saying that it is configuring Pathway Tools.

This may take a minute or so depending on the speed of your computer. The installer will then exit. You may now run Pathway Tools as follows. If you've installed Pathway Tools in your home directory, there will be a script in the pathway-tools directory named pathway-tools.

Invoke this script in the terminal window: /pathway-tools/pathway-tools This script may be copied into a location in your execution path for convenient use. For example, you could copy it into /usr/local/bin if you have that directory listed in your PATH environment variable. Then you could bring up Pathway tools by simply typing pathway-tools in an X11 terminal window. Pathway Tools can be run as an Application using AppleScript.

To do this, bring up the AppleScript editor. Select Finder-Go-Applications and then choose AppleScript-Script Editor.app.

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Enter the following code snippet into the AppleScript editor: on run do shell script '$HOME/pathway-tools/pathway-tools /dev/null 2&1 &' end run Save this in 'Application' format to your desktop and you should be able to double-click on the resulting icon to bring up Pathway Tools. You can also put this icon on your doc.

Some current Linux distributions no longer install csh or tcsh by default. This will cause the installer to fail with a cryptic error message or even fail silently. Type which csh Your computer should respond: /bin/csh Although we bundle the Motif library for Pathway Tools, we do not bundle the core X11 libraries that motif depends on. Depending on which Linux distribution you're running, you'll need to install the appropriate libraries. This is especially true for the tier1-tier2-tier3 distribution since it does not include an installer. For example, in Ubuntu 12.04, you can satisfy the library dependencies by running: apt-get install libx11-6 libxext6 libxft2 libxmu6 libxp6 libxt6 For version Ubuntu 16.04 based Linux distros, you can satisfy the library requirements by just installing the libxm4 package and its dependencies: apt-get install libmotif4 For Ubuntu 18.04 you should be able to install with just apt-get install libxm4 For CentOS 7 and similar Redhat-based distributions, this works: yum install motif.

Decide where to install Pathway Tools. For a single user, your home directory is strongly recommended. Download the Pathway Tools distribution file. These files are of the form pathway-tools-version-platform-edition-install where version is 15.0 for this release, platform could be 'linux' or 'linux-64', and edition could be 'collaborator', 'nav-path-ed-tier1' and so on. An example would be pathway-tools-15.0-linux-tier1-install If you are downloading the tier1-tier2-tier3 version of Pathway Tools for a 64-bit Linux machine, it will be in a tarball called ptools-linux64.tar.bz2. This distribution contains hundreds of organism-specific databases, and requires special installation instructions. Please proceed to the section.

The URLs pointing to these distributions can be found in the confirmation email that is sent after signing the license agreement. Please retain this email, as the same URLs will be used for every new release. Please also ensure that the correct distribution is selected for your specific platform. The distribution files are executable installers. Run the file from the command line in the normal way: $./pathway-tools-15.0-linux-tier1-install You may need to first run $ chmod u+x pathway-tools-15.0-linux-tier1-install in order to make the file executable.

A GUI-based installer will guide you through the installation process. First, it will ask you if you want to install Pathway Tools on your computer. The installer will suggest you close all applications before continuing and give you the opportunity to cancel the installation. Click Next. The installer will ask you where you want to install the Pathway Tools system files.

If you are running as a normal user, it will suggest a location in your home directory. If you are installing as the root user, it will suggest /usr/local/pathway-tools as a location.

The latter is convenient if many users will be using Pathway Tools. If the suggested locations are not suitable, click on the Browse button to navigate to a more appropriate location. Click Next once you have chosen a suitable location. Pathway Tools requires a directory where it will store local user data such as created PGDBs and HTML customization files. The installer will ask you to specify a directory path where Pathway Tools can create this 'ptools-local' directory.

Please make sure that all users who will update PGDBs have write permission to the ptools-local directory and its subdirectories. The default directory is the home directory of whoever is running the installer, which means that the data will reside in a directory called /ptools-local. If you are installing for multiple users, a directory such as /var might be more appropriate. IMPORTANT NOTES. Do not install the ptools-local directory under your Pathway Tools installation directory, since the data in this directory would then be deleted when Pathway Tools is upgraded or reinstalled.

If you are using Pathway Tools as a single user, do not use /var as your installation directory unless you are able to give yourself write access to the ptools-local directory and its contents. Instead use your home directory (this should be the default if you are not installing as the root user). Click Next once you have chosen a suitable location.

The system will pop up a dialog describing the installation. If the information it gives is not suitable, you can click the Back button to revisit previous dialogs. At this point, if you have a previous installation of Pathway Tools, you will see a dialog asking if the installer can remove this previous installation. It is highly recommended that you allow the installer to remove the previous installation. Correct operation cannot be ensured if you install Pathway Tools without removing the previous installation. Unless you are installing Pathway Tools in a different location from the previous installation, click Yes to allow the installer to remove the previous installation. The uninstaller for the previous installation will run.

Follow the instructions it presents. Once the uninstaller is finished, the installer will procede to install the files for Pathway Tools. Once the files are installed, the installer will pop up a pane reminding you of the location of the ptools-local directory. After a successful installation of Pathway Tools, a file with initialization parameters will have been written in this directory, retaining values from a prior installation if possible. The resulting file can be found in ptools-local/ptools-init.dat. This file may be customized and edited to define additional parameters specific to your site. Please see the Pathway Tools User Guide for more details on how to customize the ptools-init.dat file.

Click Finish to finish installing Pathway Tools. The installer will then pop up a banner saying that it is configuring Pathway Tools. This may take a minute or so depending on the speed of your computer. The installer will then exit. If you inadvertently skipped Oracle or MySQL configuration when you were visiting the previous web page, and you've decided to use a RDBMS, be sure to configure it now. Verify that Pathway Tools works by briefly running it (assuming it is installed in /usr/local/pathway-tools): /usr/local/pathway-tools/pathway-tools.

To allow users to easily start up this program by simply typing pathway-tools, the script in the install directory can be copied into a location accessible by all users. Access as the root user is necessary for this step. Assuming the pathway-tools directory is located in /usr/local and user-accessible binaries in /usr/local/bin, execute the following command: rm -f /usr/local/bin/pathway-tools cp /usr/local/pathway-tools/pathway-tools /usr/local/bin/pathway-tools chmod 755 /usr/local/bin/pathway-tools. Remote Access: Users often like to run Pathway Tools on a fast server and have the windows display on their desktop machine. For this to happen, the X server running on the desktop must allow remote connections. By default, most current versions of Linux do not configure the X Server to accept remote connections over the network.

If you wish to run Pathway Tools on a server and have its windows show up on your local display, you must do one of the following. Debian and Ubuntu systems need the string '-nolisten tcp' removed from all files in /etc/X11/ and its subdirectories in which the string occurs. Likewise for modern versions of Linux from the RedHat family, X Server security has been tightend. To get around this, the file /etc/X11/gdm/gdm.conf can be edited, to set: DisallowTCP=false. A different method around these X Server restrictions is to log into the computer with SSH using the -X flag (the -X flag enables forwarding X11 connections): ssh -X localhost Sometimes the -X argument will not work; in that case using -Y instead may work.

For example, displaying Pathway Tools windows remotely on a Mac system seems to require the -Y argument. The -Y argument causes the forwarded connection to be 'trusted'. Ssh -Y localhost Then, launch Pathway tools from within this session.

Due to limitations in our installer software, we use the old tarball method distribution of the full tier1-tier2-tier3 configuration. This configuration contains more than 3500 organisms and requires a large amount of memory. You will not be able to run this configuration unless you have at least 32GB (gigabytes) of physical memory (RAM); more memory will be even better. Because of its large resource requirements, we do not recommend you use this configuration unless you require access to large numbers of organism databases. Note that you can download individual organism databases from the and add them to a tier1 or tier1-tier2 configuration that does not have very large memory requirements. Follow these instructions to install:. Determine where you wish to install the software.

At least 200 GB of disk space is required to unpack this software. Save the distribution file into a convenient directory (here or elsewhere). Change directory to the place where you wish to install the software. Extract the distribution: tar jxvf.path to tarball. Run the configuration command:./aic-export/pathway-tools/ptools/18.0/install/config-ptools This will ask you for the location of the 'ptools-local' directory.

If you are installing for many users, the /var directory might be a suitable place for this directory. If you are installing for a single user, that user's home directory might be appropriate. Enter pathname of Pathway Tools local directory: /homedir/gilham. See in the instructions above for instructions on creating a script for easy execution of Pathway Tools.

Once the software exits the configuration step, your system will be ready for use. The Pathway Tools User's Guide documents the many ways you can configure the ptools-init.dat file to run Pathway Tools (including as a web server). That document is available within the Pathway Tools 'Help' menu and for this release (18.0) is stored at: pathway-tools/aic-export/pathway-tools/ptools/18.0/doc/manuals/UserGuide.pdf ©2017 SRI International, 333 Ravenswood Avenue, Menlo Park, CA SRI International is an independent, nonprofit corporation.