Re: [galaxy-user] Install Galaxy on Mac

[Edward Turk]

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
On Aug 10, 2012, at 1:41 PM, Jennifer Jackson wrote:

> 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
> 
> On 8/10/12 9:59 AM, Jennifer Jackson wrote:
>> 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-...@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
>> 
>> On 8/10/12 8:53 AM, Edward Turk wrote:
>>> 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
>>> On Aug 10, 2012, at 11:36 AM, Jennifer Jackson wrote:
>>> 
 Hi Edward -
 
 This may sound very

Re: [galaxy-user] Install Galaxy on Mac

[Hotz, Hans-Rudolf]

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



On 08/10/2012 02:37 PM, Edward Turk wrote:
> Hello,
> Could someone provide instructions for installing galaxy on a Mac OS 10.7? The
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?
> Thank you,
> Edward
> ___
> The Galaxy User list should be used for the discussion of
> Galaxy analysis and other features on the public server
> at usegalaxy.org.  Please keep all replies on the list by
> using "reply all" in your mail client.  For discussion of
> local Galaxy instances and the Galaxy source code, please
> use the Galaxy Development list:
>
>http://lists.bx.psu.edu/listinfo/galaxy-dev
>
> To manage your subscriptions to this and other Galaxy lists,
> please use the interface at:
>
>http://lists.bx.psu.edu/
>


___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

  http://lists.bx.psu.edu/

Re: [galaxy-user] Install Galaxy on Mac

[Jennifer Jackson]

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/WorkflowsAndAPI

Best,

Jen
Galaxy team


On 8/10/12 1:31 PM, Ted Goldstein wrote:

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

On Aug 10, 2012, at 1:06 PM, Jennifer Jackson wrote:


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



On 8/10/12 8:53 AM, Diana Cox-Foster wrote:

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: dx...@psu.edu
office phone: 814-865-1022
dept. phone: 814-865-1895



--
Jennifer Jackson
http://galaxyproject.org
___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

http://lists.bx.psu.edu/





--
Jennifer Jackson
http://galaxyproject.org
___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

 http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

 http://lists.bx.psu.edu/

Re: [galaxy-user] Install Galaxy on Mac

[Ted Goldstein]

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

On Aug 10, 2012, at 1:06 PM, Jennifer Jackson wrote:

> 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
> 
> 
> 
> On 8/10/12 8:53 AM, Diana Cox-Foster wrote:
>> 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: dx...@psu.edu
>> office phone: 814-865-1022
>> dept. phone: 814-865-1895
>> 
> 
> -- 
> Jennifer Jackson
> http://galaxyproject.org
> ___
> The Galaxy User list should be used for the discussion of
> Galaxy analysis and other features on the public server
> at usegalaxy.org.  Please keep all replies on the list by
> using "reply all" in your mail client.  For discussion of
> local Galaxy instances and the Galaxy source code, please
> use the Galaxy Development list:
> 
> http://lists.bx.psu.edu/listinfo/galaxy-dev
> 
> To manage your subscriptions to this and other Galaxy lists,
> please use the interface at:
> 
> http://lists.bx.psu.edu/


___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

  http://lists.bx.psu.edu/

Re: [galaxy-user] Install Galaxy on Mac

[Jennifer Jackson]

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



On 8/10/12 8:53 AM, Diana Cox-Foster wrote:

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: dx...@psu.edu
office phone: 814-865-1022
dept. phone: 814-865-1895



--
Jennifer Jackson
http://galaxyproject.org
___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

 http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

 http://lists.bx.psu.edu/

Re: [galaxy-user] Install Galaxy on Mac

[Edward Turk]

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
On Aug 10, 2012, at 1:41 PM, Jennifer Jackson wrote:

> 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
> 
> On 8/10/12 9:59 AM, Jennifer Jackson wrote:
>> 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-...@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
>> 
>> On 8/10/12 8:53 AM, Edward Turk wrote:
>>> 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
>>> On Aug 10, 2012, at 11:36 AM, Jennifer Jackson wrote:
>>> 
 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 

Re: [galaxy-user] Install Galaxy on Mac

[Jennifer Jackson]

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

On 8/10/12 9:59 AM, Jennifer Jackson wrote:

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-...@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

On 8/10/12 8:53 AM, Edward Turk wrote:

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
On Aug 10, 2012, at 11:36 AM, Jennifer Jackson wrote:


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

On 8/10/12 8:00 AM, Edward Turk 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*
On Aug 10, 2012, at 8:58 AM, Hotz, Hans-Rudolf 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



On 08/10/2012 02:37 PM, Edward Turk wrote:

Hello,
Could someone provide instructions for installing galaxy on a Mac OS
10.7? The

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?

Thank you,
Edward
___
The Gal

Re: [galaxy-user] Install Galaxy on Mac

[Jennifer Jackson]

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-...@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

On 8/10/12 8:53 AM, Edward Turk wrote:

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
On Aug 10, 2012, at 11:36 AM, Jennifer Jackson wrote:


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

On 8/10/12 8:00 AM, Edward Turk 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*
On Aug 10, 2012, at 8:58 AM, Hotz, Hans-Rudolf 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



On 08/10/2012 02:37 PM, Edward Turk wrote:

Hello,
Could someone provide instructions for installing galaxy on a Mac OS
10.7? The

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?

Thank you,
Edward
___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org .  Please keep all replies
on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

http://lists.bx.psu.edu/







___
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Galaxy analysis and other 

Re: [galaxy-user] Install Galaxy on Mac

[Diana Cox-Foster]

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: dx...@psu.edu
office phone: 814-865-1022
dept. phone: 814-865-1895



On Aug 10, 2012, at 11:36 AM, Jennifer Jackson wrote:

> 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
> 
> On 8/10/12 8:00 AM, Edward Turk 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*
>> On Aug 10, 2012, at 8:58 AM, Hotz, Hans-Rudolf 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
>>> 
>>> 
>>> 
>>> On 08/10/2012 02:37 PM, Edward Turk wrote:
 Hello,
 Could someone provide instructions for installing galaxy on a Mac OS
 10.7? The
>>> 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?
 Thank you,
 Edward
 ___
 The Galaxy User list should be used for the discussion of
 Galaxy analysis and other features on the public server
 at usegalaxy.org.  Please keep all replies on the list by
 using "reply all" in your mail client.  For discussion of
 local Galaxy instances and the Galaxy source code, please
 use the Galaxy Development list:
 
  http://lists.bx.psu.edu/listinfo/galaxy-dev
 
 To manage your subscriptions to this and other Galaxy lists,
 please use the interface at:
 
  http://lists.bx.psu.edu/
 
>>> 
>> 
>> 
>> 
>> ___
>> The Galaxy User list should be used for the discussion of
>> Galaxy analysis and other features on the public server
>> at usegalaxy.org.  Please keep all replies on the list by
>> using "reply all" in your mail client.  For discussion of
>> local Galaxy instances and the Galaxy source code, please
>> use the Galaxy Development list:
>> 
>>   http://lists.bx.psu.edu/listinfo/galaxy-dev
>> 
>> To manage your subscriptions to this and other Galaxy lists,
>> please use the interface at:
>> 
>>   http://lists.bx.psu.edu/
>> 
> 
> -- 
> Jennifer Jackson
> http://galaxyproject.org
> ___
> The Galaxy User list should be used for the discussion of
> Galaxy analysis and other features on the public server
> at usegalaxy.org.  Please keep all replies on the list by
> using "reply all" in your mail client.  For discussion of
> local Galaxy instances and the Galaxy source code, please
> use the Galaxy Development list:
> 
> http://lists.bx.psu.edu/listinfo/galaxy-dev
> 
> To manage your subscriptions to this and other Galaxy lists,
> please use the interface at:
> 
> http://lists.bx.psu.edu/


___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the inte

Re: [galaxy-user] Install Galaxy on Mac

[Edward Turk]

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
On Aug 10, 2012, at 11:36 AM, Jennifer Jackson wrote:

> 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
> 
> On 8/10/12 8:00 AM, Edward Turk 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*
>> On Aug 10, 2012, at 8:58 AM, Hotz, Hans-Rudolf 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
>>> 
>>> 
>>> 
>>> On 08/10/2012 02:37 PM, Edward Turk wrote:
 Hello,
 Could someone provide instructions for installing galaxy on a Mac OS
 10.7? The
>>> 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?
 Thank you,
 Edward
 ___
 The Galaxy User list should be used for the discussion of
 Galaxy analysis and other features on the public server
 at usegalaxy.org.  Please keep all replies on the list by
 using "reply all" in your mail client.  For discussion of
 local Galaxy instances and the Galaxy source code, please
 use the Galaxy Development list:
 
  http://lists.bx.psu.edu/listinfo/galaxy-dev
 
 To manage your subscriptions to this and other Galaxy lists,
 please use the interface at:
 
  http://lists.bx.psu.edu/
 
>>> 
>> 
>> 
>> 
>> ___
>> The Galaxy User list should be used for the discussion of
>> Galaxy analysis and other features on the public server
>> at usegalaxy.org.  Please keep all replies on the list by
>> using "reply all" in your mail client.  For discussion of
>> local Galaxy instances and the Galaxy source code, please
>> use the Galaxy Development list:
>> 
>>   http://lists.bx.psu.edu/listinfo/galaxy-dev
>> 
>> To manage your subscriptions to this and other Galaxy lists,
>> please use the interface at:
>> 
>>   http://lists.bx.psu.edu/
>> 
> 
> -- 
> Jennifer Jackson
> http://galaxyproject.org

___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

  http://lists.bx.psu.edu/

Re: [galaxy-user] Install Galaxy on Mac

[Jennifer Jackson]

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

On 8/10/12 8:00 AM, Edward Turk 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*
On Aug 10, 2012, at 8:58 AM, Hotz, Hans-Rudolf 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



On 08/10/2012 02:37 PM, Edward Turk wrote:

Hello,
Could someone provide instructions for installing galaxy on a Mac OS
10.7? The

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?

Thank you,
Edward
___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

  http://lists.bx.psu.edu/







___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

   http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

   http://lists.bx.psu.edu/



--
Jennifer Jackson
http://galaxyproject.org
___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

 http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

 http://lists.bx.psu.edu/

Re: [galaxy-user] Install Galaxy on Mac

[Edward Turk]

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
On Aug 10, 2012, at 8:58 AM, Hotz, Hans-Rudolf 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
> 
> 
> 
> On 08/10/2012 02:37 PM, Edward Turk wrote:
>> Hello,
>> Could someone provide instructions for installing galaxy on a Mac OS 10.7? 
>> The
> 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?
>> Thank you,
>> Edward
>> ___
>> The Galaxy User list should be used for the discussion of
>> Galaxy analysis and other features on the public server
>> at usegalaxy.org.  Please keep all replies on the list by
>> using "reply all" in your mail client.  For discussion of
>> local Galaxy instances and the Galaxy source code, please
>> use the Galaxy Development list:
>> 
>>   http://lists.bx.psu.edu/listinfo/galaxy-dev
>> 
>> To manage your subscriptions to this and other Galaxy lists,
>> please use the interface at:
>> 
>>   http://lists.bx.psu.edu/
>> 
> 

___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

  http://lists.bx.psu.edu/

[galaxy-user] Install Galaxy on Mac

[Edward Turk]

Hello,
Could someone provide instructions for installing galaxy on a Mac OS 10.7? The 
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?
Thank you,
Edward
___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

  http://lists.bx.psu.edu/