Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • Galaxy in Linux

    Hello Everyone,

    Quick question. I have used galaxy before to run blastn and blastx (the gui web version). I know want to try using Galaxy installed in linux (the command mode version).
    Does anyone know where to find a tutorial on this (I need things like what commands to use to make the blast run). The cluster I am using has galaxy version 1 and 2 installed and I have no idea how to start running it. Any help will be helpful and very much appreciated

    Thank you in advance!

  • #2
    The command line manual for BLAST+ is here: http://www.ncbi.nlm.nih.gov/books/NBK1763/

    Blast family of programs must be installed on your cluster (or you could easily request your cluster administrators to install it by using the code source found at a link in the blast manual linked above). If you are new to command line the easiest thing to do would be to ask the admins for the location of the executables.

    You will need to download a copy of the blast index files (at lease ones that you need). It is easiest to download the pre-built versions from this link: ftp://ftp.ncbi.nih.gov/blast/db/ There is also a nice script available that the cluster admins can use to keep the indexes automatically synced with NBCI at a set interval (daily, weekly etc).

    You will want to understand the syntax for the job scheduler for your cluster to submit the jobs.

    Comment


    • #3
      you start galaxy by navigating to the galaxy directory and use

      sh run.sh

      Comment

      Latest Articles

      Collapse

      • seqadmin
        Multiomics Techniques Advancing Disease Research
        by seqadmin


        New and advanced multiomics tools and technologies have opened new avenues of research and markedly enhanced various disciplines such as disease research and precision medicine1. The practice of merging diverse data from various ‘omes increasingly provides a more holistic understanding of biological systems. As Maddison Masaeli, Co-Founder and CEO at Deepcell, aptly noted, “You can't explain biology in its complex form with one modality.”

        A major leap in the field has
        ...
        02-08-2024, 06:33 AM
      • seqadmin
        The 3D Genome: New Technologies and Emerging Insights
        by seqadmin


        The study of three-dimensional (3D) genomics explores the spatial structure of genomes and their role in processes like gene expression and DNA replication. By employing innovative technologies, researchers can study these arrangements to discover their role in various biological processes. Scientists continue to find new ways in which the organization of DNA is involved in processes like development1 and disease2.

        Basic Organization and Structure
        Understanding...
        01-22-2024, 03:25 PM

      ad_right_rmr

      Collapse

      News

      Collapse

      Topics Statistics Last Post
      Started by seqadmin, Yesterday, 08:57 AM
      0 responses
      12 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 02-14-2024, 09:19 AM
      0 responses
      43 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 02-12-2024, 03:37 PM
      0 responses
      408 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 02-09-2024, 03:36 PM
      0 responses
      648 views
      0 likes
      Last Post seqadmin  
      Working...
      X