IGM IT – Page 6

HPC – Lampredi – software update – Trinity 20130814

Oct 012013

Trinity has been updated to version 2013-08-14. Details are:

$ module load apps/trinity/20130814 apps/trinity/20130814/gcc-4.4.6 | -- libs/gcc/system | * --> OK | OK


----------------------------------------------------------------------------------
$ ls $TRINITYDIR

Analysis   docs           install_tests.sh  notes    PerlLibAdaptors  sample_data      util

Butterfly  galaxy-plugin  LICENSE.txt       perl     README           Trinity.pl

Chrysalis  Inchworm       Makefile          PerlLib  Release.Notes    trinity-plugins
----------------------------------------------------------------------------------
$ module whatis apps/trinity/20130814

apps/trinity/20130814: 
            Title: trinity

          Summary: A novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data

          License: BSD

            Group: Bioinformatics

              URL: http://trinityrnaseq.sourceforge.net/
             Name: trinity

          Version: 20130814

           Module: apps/trinity/20130814/gcc-4.4.6

      Module path: /opt/gridware/etc/modules/apps/trinity/20130814/gcc-4.4.6

     Package path: /opt/gridware/pkg/apps/trinity/20130814/gcc-4.4.6
       Repository: git+http://download.alces-software.com/git/packager-base@0fda8da

          Package: apps/trinity/20130814@8c2c4fe7

      Last update: 2013-10-01
          Builder: root@headnode1.lampredi.cluster.local

       Build date: 2013-10-01T12:04:20

    Build modules: apps/cpanminus/1.5017/noarch

         Compiler: compilers/gcc/system

           System: Linux 2.6.32-279.2.1.el6_lustre.gc46c389.x86_64 x86_64

             Arch: Intel(R) Xeon(R) CPU E5620 @ 2.40GHz, 2x4 (b6b89932)

     Dependencies: libs/gcc/system (using: libs/gcc/system)
For further information, execute:
	module help apps/trinity/20130814/gcc-4.4.6
----------------------------------------------------------------------------------
$ module help apps/trinity/20130814/gcc-4.4.6
----------- Module Specific Help for 'apps/trinity/20130814/gcc-4.4.6' -----------
                      ======== trinity ========

        A novel method for the efficient and robust de novo

         reconstruction of transcriptomes from RNA-seq data

                      ========================                      
This module sets up your environment for the use of the 'trinity'

application. This module sets up version '20130814' of the

application.
>> SYNOPSIS <> LICENSING <> FURTHER INFORMATION <> GET STARTED <<
Please refer to the website for further details on usage of this

package.
----------------------------------------------------------------------------------
$ module show apps/trinity/20130814/gcc-4.4.6

-------------------------------------------------------------------

/opt/gridware/etc/modules/apps/trinity/20130814/gcc-4.4.6:
module-whatis	 
            Title: trinity

          Summary: A novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data

          License: BSD

            Group: Bioinformatics

              URL: http://trinityrnaseq.sourceforge.net/
             Name: trinity

          Version: 20130814

           Module: apps/trinity/20130814/gcc-4.4.6

      Module path: /opt/gridware/etc/modules/apps/trinity/20130814/gcc-4.4.6

     Package path: /opt/gridware/pkg/apps/trinity/20130814/gcc-4.4.6
       Repository: git+http://download.alces-software.com/git/packager-base@0fda8da

          Package: apps/trinity/20130814@8c2c4fe7

      Last update: 2013-10-01
          Builder: root@headnode1.lampredi.cluster.local

       Build date: 2013-10-01T12:04:20

    Build modules: apps/cpanminus/1.5017/noarch

         Compiler: compilers/gcc/system

           System: Linux 2.6.32-279.2.1.el6_lustre.gc46c389.x86_64 x86_64

             Arch: Intel(R) Xeon(R) CPU E5620 @ 2.40GHz, 2x4 (b6b89932)

     Dependencies: libs/gcc/system (using: libs/gcc/system)
For further information, execute:
	module help apps/trinity/20130814/gcc-4.4.6

module-prereq libs/gcc/system module-conflict apps/trinity setenv TRINITYDIR /opt/gridware/pkg/apps/trinity/20130814/gcc-4.4.6 setenv TRINITYBIN /opt/gridware/pkg/apps/trinity/20130814/gcc-4.4.6 prepend-path PERL5LIB /opt/gridware/pkg/apps/trinity/20130814/gcc-4.4.6/perl/lib/perl5 prepend-path MANPATH /opt/gridware/pkg/apps/trinity/20130814/gcc-4.4.6/perl/man prepend-path PATH /opt/gridware/pkg/apps/trinity/20130814/gcc-4.4.6/perl/bin prepend-path PATH /opt/gridware/pkg/apps/trinity/20130814/gcc-4.4.6/util prepend-path PATH /opt/gridware/pkg/apps/trinity/20130814/gcc-4.4.6 ----------------------------------------------------------------------------------

Lampredi HPC
igm-lampredi-users@ncl.ac.uk

IGM IT
igmithelp@ncl.ac.uk
x8625

Flow Cytometry – Off-campus access to data using WEBFOLDERS

Uncategorized No Responses »

Jul 192013

Webfolders allow you to access your data when off-campus. Below are instructions on how to access the two FCCF data areas, typically called the S: drive (live instrument data) and the R: drive (archived data).

They can be used with any Internet ready computer, regardless of your location, and are also useful when used with non-University computers that are based on-campus.

__________________________________________________________________

*** Windows 7

FCCF S: DRIVE / Live instrument data

Click the Windows icon, on the task bar
Click Computer
Click “Map network drive”
Click the link “Connect to a Web site that you can use to store your documents…”
Click Next button
Click Next button
Enter the address:

https://webfolders.ncl.ac.uk/scratch/IHGSCRATCH/FLOWCF

Click Next button
When prompted, enter your University username using this format:

campus\nabc123

It is important that you precede your username with campus\

Enter your University login and tick the “Remember my credentials” box
Click OK button
Enter a name for this folder. For example, FCCF S DRIVE
Click Next button
Click Finish button

The FCCF R: DRIVE / archived data

Click the Windows icon, on the task bar

Click Computer
Click “Map network drive”
Click the link “Connect to a Web site that you can use to store your documents…”
Click Next button
Click Next button
Enter the address:

https://webfolders.ncl.ac.uk/igm/FLOWCF

Click Next button
When prompted, enter your University username using this format:

campus\nabc123

It is important that you precede your username with campus\

Enter your University username and tick the “Remember my credentials” box
Click OK button
Enter a name for this folder. For example, FCCF R DRIVE
Click Next button
Click Finish button

__________________________________________________________________

*** Apple Mac OS X

FCCF S: DRIVE / live instrument data

Click on your desktop area
Finder (menu bar)
Preferences
Ensure that “Connected Servers” box is ticked
Close the window

Go (menu bar)
Connect to Server…
Carefully enter this address:

https://webfolders.ncl.ac.uk/scratch/IHGSCRATCH/FLOWCF

Click + icon
Click Connect button
Enter your University username and password
Tick the box next to “Remember this password in my keychain”
Click Connect button

FCCF R: DRIVE / archived area

Click on your desktop area
Finder (menu bar)
Preferences
Ensure that “Connected Servers” box is ticked
Close the window

Go (menu bar)
Connect to Server…
Carefully enter this address:

https://webfolders.ncl.ac.uk/igm/FLOWCF

Click + icon
Click Connect button
Enter your University username and password
Tick the box next to “Remember this password in my keychain”
Click Connect button

__________________________________________________________________

Webfolders – Your H: drive

Uncategorized No Responses »

Jul 112013

You can access your H: drive via something called “webfolders”. This works on any Internet capable Windows/Mac/Linux computer, both on and off campus.

Webfolders are a useful alternative to RAS, and they allow non University Common Desktop PCs access to your H: drive and Z: drive, regardless of your location.

You can also use webfolders to access Institute folders and Research folders (more commonly known as the Z: drive). We have a different set of instructions here explaining how to access those areas.

__________________________________________

Accessing your H: drive / home folder

*** Windows 7 / XP

Users should follow the instructions provided by ISS http://www.ncl.ac.uk/itservice/filestore/remoteaccess/webfolders/

*** Apple Mac OS X

Finding your Home Folder / Webfolders path

Open the Newcastle university home page: http://www.ncl.ac.uk
Click People search
Click My Details
If prompted, authenticate using your campus ID and password.
Click the link for “ISS technical information, including details of which ISS servers you use and any role accounts you own.”
Either make a note or right-click on the link next to “Home folder via WebFolders” and choose “Copy link” from the menu
Close your web browser

Click on your desktop area
Finder (menu bar)
Preferences
Ensure that “Connected Servers” box is ticked
Close the window

Go (menu bar)
Connect to Server…
Carefully enter the address you noted earlier or delete whatever address is currently in the Server Address box. Right-click and choose “Paste” from the menu

You should end up with something that resembles
https://webfolders.ncl.ac.uk/home/homeXX/n123example

Click Connect button
Enter your ISS login and password
Tick “remember this password in my keychain”
Click Connect button

*** Linux

This has only been tested on our officially supported Linux distributions – Red Hat/CentOS/Scientific Linux/Fedora. We will test other distributions later.

Follow the first part of the Apple Mac instructions, with regards to finding your Home Folder/Webfolder path

Places (menu bar)
Connect to Server…
Service type = Secure WebDAV (HTTPS)
Server = webfolders.ncl.ac.uk
Folder = /home/homeXX/n123example
(replace homeXX, which can be found in the webfolder address you noted earlier, and n123example should be altered to reflect your ISS login

username = your ISS login
Name to use for connection = something useful eg h drive
Click Connect button
Enter your ISS password. Tick “remember my password for this session”
Click Connect button
Click “Allow Once” button

When finished, remember to unmount your webfolder. Right-click over the web folder icon, sitting on the Desktop, and choose “Unmount Volume” from the menu.

Webfolders – Institute and Research folders (Z: drive)

Uncategorized No Responses »

Jul 112013

You can access your H: drive, the Institute folders and research folders via something called “webfolders”. This works on any Internet capable Windows/Mac/Linux computer, both on and off campus.

Webfolders are a useful alternative to RAS, and they allow non University Common Desktop PCs access to your H: drive and Z: drive, regardless of your location.

Below are instructions on how to access the Z: drive/Institute folders/Research folders. We have separate instructions available here on how to access your H: drive using webfolders.

__________________________________________

Accessing the Z: drive / Institute folders / Research folders

*** Windows 7

https://webfolders.ncl.ac.uk/igm

Click Next button
When prompted, enter your ISS login using this format:

campus\n123example

It is important that you precede your login with campus\

Enter your ISS login and tick the “Remember my credentials” box
Click OK button
Enter a name for this folder. For example, IGM Z DRIVE
Click Next button
Click Finish button

This adds the webfolder to your computer. It behaves like the Z: drive on a IGM University Common Desktop computer, though there are some subtle differences.

*** Windows XP

Click the Start button, on the task bar
Click My Computer
Click Tools (menu bar)
Click “Map Network Drive…”
Click the link “Sign up for online storage or connect to…”
Click Next button
Click Next button

Enter the address:

https://webfolders.ncl.ac.uk/igm

Click Next button
When prompted, enter your ISS login using this format:

campus\n123example

It is important that you precede your login with campus\

Enter your ISS login and tick the “Remember my password” box
Click OK button
Enter a name for this folder. For example, IGM Z DRIVE
Click Next button
Click Finish button

*** Apple Mac OS X

Click on your desktop area
Finder (menu bar)
Preferences
Ensure that “Connected Servers” box is ticked
Close the window

Go (menu bar)
Connect to Server…
Carefully enter this address:

https://webfolders.ncl.ac.uk/igm

Click Connect button
Enter your ISS login and password
Tick the box next to “Remember this password in my keychain”
Click Connect button

*** Linux

This has only been tested on our officially supported Linux distributions – Red Hat/CentOS/Scientific Linux/Fedora. We will test other distributions later.

Places (menu bar)
Connect to Server…
Service type = Secure WebDAV (HTTPS)
Server = webfolders.ncl.ac.uk
folder = igm
user name = your ISS login
Name to use for connection = can be anything e.g “igm z drive”
Click Connect button
Enter your password. Tick “remember password for this session” box
Click Connect button
If prompted, choose “Allow once” when asked about “allow application access to keyring?”

When finished, remember to unmount your webfolder. Right-click over the web folder icon, sitting on the Desktop, and choose “Unmount Volume” from the menu.

Flow Cytometry – storage @ IGM guide

Uncategorized No Responses »

Oct 252012

Our remit is to provide access to data produced by the Flow Cytometry Core Facility via University Common Desktop PCs.

Below are instructions on how to map drives to the two storage areas used by the FCCF. They are commonly known as the S: drive (scratch space/live instrument data) and the R: drive (archived data).

New Flow Cytometry users must provide IGM IT with their University username (not your FCCF username, nor do we need any passwords) in advance. Failure to do this will mean that you will not have access to the data. The FCCF team are not responsible for enabling access. Hence *your* need to request access from IGM IT.

If you are a new Flow Cytometry user, please send us your request for access, along with your University login, to: igmithelp@ncl.ac.uk

We have also provided instructions for Mac users, and there are two alternative ways for you to access your data when off campus (via RAS and webfolders).

Returning to our remit, should you run into any issues when trying to access your data, we ask that you seek out a University Common Desktop computer.

Important! USB sticks/portable drives are NOT permitted within the Flow Cytometry Core Facility. This is why we have been tasked with providing you with access to the instrument data via other means.

Please do ensure that you have backups of your data. Files stored on the S: drive are removed after 90 days, in order to maintain adequate storage space for *live* instrument data. Please do contact the FCCF team about any queries you may have regarding data and any other aspects of their service, including analysis software.

Thank you for your co-operation.

IGM IT
igmithelp@ncl.ac.uk
– – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – –

Mapping the S: drive (FCCF scratch space /live instrument data)

*** Data stored on the S: drive is removed after 90 days ***

• Windows 7

Click on Windows logo (taskbar)
Click “Computer”
Click ‘Map network drive’ option
Change “Drive” option to the letter S
Change “Folder” option to:

\\campus.ncl.ac.uk\scratch\IHGSCRATCH\FLOWCF

Ensure that ‘Reconnect at logon’ is ticked
Click ‘Finish’ button and the S: drive will be mapped

• Mac OS X

Click on Desktop area.
Click on Go (menu bar)
Choose ‘Connect to server…’ and type:

smb://fsarchive.ncl.ac.uk/IHGScratch/FLOWCF

Click + icon
Click Connect
Enter University username and password
Tick ‘remember this password…’ option

IMPORTANT! Should you encounter problems using the above address, try the following alternative:
cifs://campus.ncl.ac.uk/scratch/IHGSCRATCH/FLOWCF
Some users have reported that substituting smb:// for cifs:// works for them

Additional instructions for Mac users: click on Desktop area. Click on Finder (in menu bar), choose Preferences. Ensure ‘Connected servers’ option is ticked. Close window.

Mapping the R: drive (FCCF archived data)

• Windows 7

Click on Windows logo, far left of task bar
Click “Computer”
Click ‘Map network drive’ option Change “Drive” option the letter R
Change “Folder” option to:

\\campus.ncl.ac.uk\igm\FLOWCF

Ensure that ‘Reconnect at logon’ is ticked
Click ‘Finish’ button and the R: drive will be mapped

• Mac OS X

Click on Desktop area
Click on Go (menu bar)
Choose ‘Connect to server…’ and type:

smb://fs-ncl-smb-db.ncl.ac.uk/igm-flowcf
Click + icon
Click Connect
Enter University username and password
Tick ‘remember this password…’ option

IMPORTANT! Should you encounter problems using the above address then try the following alternative:
cifs://campus.ncl.ac.uk/IGM/FLOWCF
Some users have reported that substituting smb:// for cifs:// works for them

Additional instructions for Mac users: click on Desktop area. Click on Finder (in menu bar), choose Preferences. Ensure ‘Connected servers’ option is ticked. Close window.

Accessing FCCF data when off campus

There are two options for retrieving your data, when off-campus. You may find the Webfolders option easier to use than RAS. Both work on any internet capable computer.

Accessing the FCCF data when on-campus, using a laptop (University owned or private laptop)

The instructions can be found here. It is similar to mapping drives when using a University Common Desktop PC.

However, you *must* precede your University username with campus\ otherwise you will be refused access. We cannot stress enough that you must remember to include campus\ as part of your University username, when using these instructions!

ISS Home Archive Service

Uncategorized No Responses »

Jul 122012

Your H: drive will have an upper limit of 4GB. If you need more than this then ISS ask that you consider using their “Home Archive Service”. If you are nearing your H: drive limit then you may have received an automated message from ISS about this subject.

It can be thought of as a second H: drive, providing you with 20GB of additional storage. The one condition ISS set is that this new storage area can only accept compressed files, typically called zipped files.

In other words, your H: drive would remain as your primary storage but you would move less frequently accessed files/folders from your H: drive to your new 20GB area. Those files would be compressed/zipped before you moved them there.

This feature is available on Macs (right-click your file/folder and choose ‘Compress …’) and Linux – you can use the command line or simply right-click and use the ‘Compress…’ option.

To apply for this service, click on: https://crypt.ncl.ac.uk/helpdesk/home-archive
and follow the on-screen prompts.

ISS will send you a detailed set of instructions. For Windows users, you are simply going to map a new drive. You will be asked to choose a letter to represent your new 20GB of storage. We ask that you avoid using Z, W, T, S and R, as these are reserved by the Institute.

Mac users should not feel left out! We need to convert the address ISS give you into something that your Mac understands, and we are happy to help with this.

Using both your H: drive and your new (archived) storage efficiently, you will have a combined total of 24GB of storage. For a more detailed explanation of this service please visit:

http://www.ncl.ac.uk/iss/getstarted/storage/personalarchive.php

ISS File Drop-Off service

Uncategorized No Responses »

Jul 122012

ISS have re-named their Drop-box service (for rather obvious reasons), and it is now known as the University “File Drop-Off Service”. This allows you to transfer larger file(s) between University colleagues and non-University colleagues.

Before this service existed, it was a rather complicated task to pass large files on to other people. There is currently a 20MB file size limit that is enforced on email attachments. In the past, there has often been problems sending files to people who are not members of the University. ISS designed the File Drop-Off Service to help address these matters.

This ISS service can be reached via: https://dropoff.ncl.ac.uk/

You can read a more detailed explanation at: https://dropoff.ncl.ac.uk/about.php

It’s worth noting that the file size limit for this drop-off service is 2GB (per transaction). You should always compress the files you are going to send someone first, as this not only helps reduce the overall size involved but it helps “protect” the data as it makes it way through the Internet.

All our University Common Desktop PCs can compress files/folders instantly, via right-clicking on the file/folder in question and following the “7zip” option in the menu. Choose the option “Compress to <name of your file or folder>.zip”. This feature is available on Macs (right-click your file/folder and choose ‘Compress …’) and Linux. Most computers have built-in software that can uncompress zip files, so you do not need to worry about the recipient not being able to read the your files.

The IGM does runs a similar service but it is mainly reserved for users who need to move sequencing data in and out of the Institute. Our service also requires that you speak to us first, so that we can offer you the best possible help. Depending on the size of the data involved, some transactions are required to take place over a weekend.

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