Install Galaxy On Mac

6.3 years ago by

Edward Turk • 100 wrote:

Both responses worked for checking python version, but trying to download gave an error: Install Galaxy on Mac OS10.7 1. Open Applications/Utilities/Terminal.app 2. Check Python version by pasting in "python -V", no quotes, and hit return response = Python 2.7.1 3. Get Galaxy by pasting in "% hg clone https://bitbucket.org/galaxy /galaxy-dist/", no quotes, and hit return response = -bash: fg: %: no such job

ADD COMMENT • link written 6.3 years ago by Edward Turk • 100

Hi Edward - This may sound very simple, but did the "%" get included in the command to do the download by mistake? You'll want to remove that from the command string run again (was used to note the terminal prompt, is not a part of the command). So, just this: prompt$ hg clone https://bitbucket.org/galaxy/galaxy-dist/ I just tested the galaxy-dist repository and there are no issues at bitbucket (right now). So, otherwise the MAC install should be fine. Maybe this helps? Jen Galaxy team -- Jennifer Jackson http://galaxyproject.org

ADD REPLY • link written 6.3 years ago by Jennifer Hillman Jackson ♦ 25k

Hi Jen, Yes, it is best to assume I know nothing about programming. I installed Mercurial, but don't know how to check that it was successful other than it said so. Removing % helped, but said I do not have permission: Install Galaxy on Mac OS10.7 1. Open Applications/Utilities/Terminal.app 2. Check Python version by pasting in "python -V", no quotes, and hit return response = Python 2.7.1 3. Install Mercurial Response = "Successful Installation" but I don't know how to check this 4. Get Galaxy by pasting in "hg clone https://bitbucket.org/galaxy /galaxy-dist/", no quotes, and hit return Response = warning: bitbucket.org certificate with fingerprint 24:9c:45:8b:9c:aa:ba:55:4e:01:6d:58:ff:e4:28:7d:2a:14:ae:3b not verified (check hostfingerprints or web.cacerts config setting) destination directory: galaxy-dist abort: Permission denied: /private/etc/galaxy-dist Thanks, Edward

ADD REPLY • link written 6.3 years ago by Edward Turk • 100

Hi Edward, Sorry, the "https" is probably also a problem. I thought about commenting about that before, but was wasn't sure about how much help you would need exactly or if you were logged into bitbucket or not. So please use this: prompt$ hg clone http://bitbucket.org/galaxy/galaxy-dist If you ever need to clone again or update, the commands are in the News Brief summaries + top of each full report: http://wiki.g2.bx.psu.edu/DevNewsBriefs ** Note the "%" is used here to designate the terminal prompt. This is fairly common, so now that you know, you will be able to recognize it. Also look for the "$" and ">" characters to represent the prompt at the start of a shared command line in various documents (Galaxy or other). I'll just use "prompt$" right now to be clear. For Mercurial, to confirm the install, you can type at the terminal prompt from anywhere: prompt$ hg version prompt$ hg help The "quick start" and "guide" at http://mercurial.selenic.com/ is a good place for basic hg commands. A web search will return plenty of other choices. This is the last email in this thread I think we should send to both lists - from here forward let's just cc to galaxy-dev@bx.psu.edu for follow-up and leave the user list off - no need to post to both. The other question about MAC resource we can do the same with, once answered. Best, Jen Galaxy team -- Jennifer Jackson http://galaxyproject.org

ADD REPLY • link written 6.3 years ago by Jennifer Hillman Jackson ♦ 25k

Update (and a post to both lists!) Nate pointed me to the real problem. https/http isn't a problem at bitbucket anymore. The issue is where you are installing (/etc) and write permissions. But, it is not recommended anyway. You will want to install in your home directory. To get there, type: prompt$ cd Just that will put you in your home. To see where this is on your system path, type this: prompt$ pwd To see what else is here, type: prompt$ ls A google for mac unix commands will bring up various basic help/tutorials and such as you need them. Hopefully this gets you going! Jen Galaxy team -- Jennifer Jackson http://galaxyproject.org

ADD REPLY • link written 6.3 years ago by Jennifer Hillman Jackson ♦ 25k

Jen - Getting Closer! - But not there yet. Getting Galaxy seems to have worked. Here is the last line from Terminal: mbio-edt:~ edwardturk$ cd mbio-edt:~ edwardturk$ hg clone http://bitbucket.org/galaxy/galaxy- dist warning: bitbucket.org certificate with fingerprint 24:9c:45:8b:9c:aa:ba:55:4e:01:6d:58:ff:e4:28:7d:2a:14:ae:3b not verified (check hostfingerprints or web.cacerts config setting) real URL is https://bitbucket.org/galaxy/galaxy-dist destination directory: galaxy-dist warning: bitbucket.org certificate with fingerprint 24:9c:45:8b:9c:aa:ba:55:4e:01:6d:58:ff:e4:28:7d:2a:14:ae:3b not verified (check hostfingerprints or web.cacerts config setting) requesting all changes warning: bitbucket.org certificate with fingerprint 24:9c:45:8b:9c:aa:ba:55:4e:01:6d:58:ff:e4:28:7d:2a:14:ae:3b not verified (check hostfingerprints or web.cacerts config setting) adding changesets adding manifests adding file changes added 7405 changesets with 28970 changes to 5975 files warning: bitbucket.org certificate with fingerprint 24:9c:45:8b:9c:aa:ba:55:4e:01:6d:58:ff:e4:28:7d:2a:14:ae:3b not verified (check hostfingerprints or web.cacerts config setting) warning: bitbucket.org certificate with fingerprint 24:9c:45:8b:9c:aa:ba:55:4e:01:6d:58:ff:e4:28:7d:2a:14:ae:3b not verified (check hostfingerprints or web.cacerts config setting) updating to branch default 3922 files updated, 0 files merged, 0 files removed, 0 files unresolved But then I could not start it up: mbio-edt:~ edwardturk$ sh run.sh sh: run.sh: No such file or directory Edward

ADD REPLY • link written 6.3 years ago by Edward Turk • 100

Thanks Jen, Hans, and Scott, I have it running on my laptop now and here are the steps I followed: Install Galaxy on MacBook Pro OS10.7.4 (08-10-2012) Install Mercurial http://mercurial.selenic.com/wiki/ Open Applications/Utilities/Terminal.app Confirm Mercurial installation by pasting in "hg version", no quotes and hit return response = version 2.3+20120807 Check Python version by pasting in "python -V", no quotes and hit return response = Python 2.7.1 Go to your home directory by pasting in "cd", no quotes and hit return Get Galaxy by pasting in "hg clone http://bitbucket.org/galaxy/galaxy-dist/", no quotes and hit return Go to the Galaxy directory by pasting in "cd galaxy-dist", no quotes and hit return Start up Galaxy by pasting in "sh run.sh", no quotes and hit return Open web browser and paste in http://localhost:8080, no quotes and hit return Have a nice day, Edward

ADD REPLY • link written 6.3 years ago by Edward Turk • 100

I was wondering if anyone could comment on how memory/computational intensive a local instal of Galaxy is? What type of computer (especially Macs) is needed for a local install to run fairly well? Thanks for any info--- Diana ********************************** Diana Cox-Foster, Professor office: 536 ASI Bldg MAIL: 501 ASI Bldg Department of Entomology Penn State University University Park, PA, USA 16802 email: dxc12@psu.edu office phone: 814-865-1022 dept. phone: 814-865-1895

ADD REPLY • link written 6.3 years ago by Diana Cox-Foster • 40

Hi Diana, Galaxy itself will run on any recent MAC with the basic requirements (python, mercurial, etc.). The standard set-up isn't computationally intensive at all. What makes a difference are the tools you intend to use, the size of the data (genomes, datasets, libraries), the volume of throughput, and processing speed expectations. This wiki has some general guidelines that can help you decide between how to use Galaxy (Main, Local, or Cloud) based on these and related factors: http://wiki.g2.bx.psu.edu/Big%20Picture/Choices But what would be best, to address your specific question, is if you could provide more information about what you intend to do. Others on the mailing list would likely be able to comment about what type of set-up they are using successfully for similar work. Best, Jen Galaxy team -- Jennifer Jackson http://galaxyproject.org

ADD REPLY • link written 6.3 years ago by Jennifer Hillman Jackson ♦ 25k

Hi Jen, I know we are using Mercurial for Galaxy's own source code. Is there a way for Galaxy to store and retrieve workflows from Mercurial? Thanks, Ted UCSC CBSE

ADD REPLY • link written 6.3 years ago by Ted Goldstein • 40

Hello Ted, Workflows are included in the Galaxy Main Tool Shed http://toolshed.g2.bx.psu.edu/ --> Search for workflows Documentation is in this wiki (see #22, 23, & 24): http://wiki.g2.bx.psu.edu/Tool%20Shed Other current information about workflow development can be found in the meeting notes from the 2012 GCC Breakout. http://wiki.g2.bx.psu.edu/Events/GCC2012/Program/Breakouts/WorkflowsAn dAPI Best, Jen Galaxy team -- Jennifer Jackson http://galaxyproject.org

ADD REPLY • link written 6.3 years ago by Jennifer Hillman Jackson ♦ 25k

6.3 years ago by

Hotz, Hans-Rudolf • 10

Hotz, Hans-Rudolf • 10 wrote:

Hi Edward I am moving your e-mail to 'galaxy-dev' since it's about a local Galaxy instance. I don't think there are any differences between installing Galaxy on Linux and Mac OS X. Hence you can follow the step-by-step instructions on the wiki (well, there are actually only two steps anyway...): http://wiki.g2.bx.psu.edu/Admin/Get%20Galaxy WRT checking the python version: just type 'python -V' on the command line, eg on my old MacBook: bash-3.2$ python -V Python 2.5.1 bash-3.2$ Hope this helps Regards, Hans instructions provided by galaxy start off by asking me to check my python version, but I don't know how to do that. I figure someone has step- by-step instructions or a screen cast?

ADD COMMENT • link written 6.3 years ago by Hotz, Hans-Rudolf • 10

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