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anthill_sri015 [2020/05/27 00:04] – tmatejukanthill_sri015 [2023/08/01 01:08] (current) – external edit 127.0.0.1
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 ==== prefetch 2.8.2 ==== ==== prefetch 2.8.2 ====
-Anhill's computing nodes offer ''prefetch'' in version 2.8.2 (from ''sra-tools'' package). If you would like to use newer version it is available at https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software .+Anthill's computing nodes offer ''prefetch'' in version 2.8.2 (from ''sra-tools'' package). If you would like to use newer version it is available at https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software .
  
 ==== prefetch configuration ==== ==== prefetch configuration ====
-Default path where prefetch downloads files is ''~/ncbi/''. Files you download from NCBI will be rather big, so it is a good idea to change this path to ''/workspace/${USER}'' where usually more space is available. To do this start interactive session, create new folder and then use ''vdb-config'' command to change download folder. You can use ''vdb-config -i'' to inspect other options in tui mode.+Default path where prefetch downloads files is ''~/ncbi/''. Files you download from NCBI will be rather big, so it is a good idea to change this path to ''/workspace/${USER}'' where usually more space is available. To do this start interactive session, create new folder and then use ''vdb-config'' command to change download folder (you can use ''vdb-config -i'' to inspect other configuration options in tui mode).
   jsmith@anthill23:~$ srun --pty bash -l   jsmith@anthill23:~$ srun --pty bash -l
   jsmith@ant009:~$ mkdir -p /workspace/${USER}/ncbi   jsmith@ant009:~$ mkdir -p /workspace/${USER}/ncbi
-  jsmith@ant009:~$ vdb-config --set default-path=/workspace/${USER}/tmp_ncbi+  jsmith@ant009:~$ vdb-config --set default-path=/workspace/${USER}/ncbi
   jsmith@ant009:~$ exit   jsmith@ant009:~$ exit
   jsmith@anthill23:~$      jsmith@anthill23:~$   
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 ==== aspera 3.9.6 (test) ==== ==== aspera 3.9.6 (test) ====
-After aspera cli installation test with bellow commands:+After aspera cli installation, test it with bellow commands:
  
   jsmith@anthill23:~$ export PATH=/home/users/${USER}/.aspera/cli/bin:$PATH   jsmith@anthill23:~$ export PATH=/home/users/${USER}/.aspera/cli/bin:$PATH
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 ==== sbatch example ==== ==== sbatch example ====
-Whith this sbatch file you can use anthill's computing node to download ''SRR390728' with prefetch and ascp transport protocol.+Whith this sbatch file you can use anthill's computing node to download ''SRR390728'' with prefetch and ascp as transport protocol.
   #!/bin/bash -l   #!/bin/bash -l
   #SBATCH --partition=short   #SBATCH --partition=short
   #SBATCH --ntasks=1   #SBATCH --ntasks=1
-  #SBATCH --mem 4G+  #SBATCH --mem 3G
   #SBATCH --job-name SRR390728   #SBATCH --job-name SRR390728
      
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   FILENAME="SRR390728"   FILENAME="SRR390728"
 +  
   echo "date: `date -R`"   echo "date: `date -R`"
   echo "host: `hostname`"   echo "host: `hostname`"
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 Please remember to not to overuse Internet connections of CeNT or NCBI when downloading files. Do not start dozens of download processes at once, this will stress Internet connections both of CeNT and NCBI. Be aware that some organizations recognize massive download as DOS attack and will block access (temporary or permanently) to its resources. Please remember to not to overuse Internet connections of CeNT or NCBI when downloading files. Do not start dozens of download processes at once, this will stress Internet connections both of CeNT and NCBI. Be aware that some organizations recognize massive download as DOS attack and will block access (temporary or permanently) to its resources.
  
-  --- \\ + 
-*) [https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=toolkit_doc&f=prefetch] \\ +*) https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=toolkit_doc&f=prefetch \\ 
-*) [http://download.asperasoft.com/download/docs/cli/3.9.6/user_linux/pdf2/Aspera_CLI_Admin_3.9.6_Linux.pdf] \\ +*) http://download.asperasoft.com/download/docs/cli/3.9.6/user_linux/pdf2/Aspera_CLI_Admin_3.9.6_Linux.pdf \\ 
-*) [https://www.ncbi.nlm.nih.gov/] \\+*) https://www.ncbi.nlm.nih.gov/ \\
  
anthill_sri015.1590530669.txt.gz · Last modified: 2023/08/01 06:38 (external edit)

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