Differences

This shows you the differences between two versions of the page.

--- howto:bioinformatics [2015/10/01 11:49]
dane [bowtie] fixing -o and -e #PBS options.
+++ howto:bioinformatics [2025/05/21 10:50] (current)
nmfuphi [Singularity]
@@ Line 1: / Line 1: @@
 ====== Bioinformatics at the CHPC ======
-Welcome to the bioinformatics at the CHPC wiki page! This page describes the basic procedures involved in getting your programs running at the CHPC rather than a description of how to do any particular bioinformatics analysis. If anything is unclear please hover your mouse over the superscripts! ((Because they might just give you some hints ;-))) For the most part we will be assuming you have at least a little familiarity with Linux. Much of this information is available elsewhere in the CHPC's wiki (probably in more detail), but here we are trying to have everything accessible in one place for the bioinformatics community.
-The Bioinformatics Service Platform (BSP) has recently obtained its own domain and website at http://bsp.ac.za/. We also host Globus endpoints at chpcbio#bio.chpc.ac.za and chpcbio#globus.chpc.ac.za.
+Welcome to the bioinformatics at the CHPC wiki page! This page describes the basic procedures involved in getting your programs running at the CHPC rather than a description of how to do any particular bioinformatics analysis. If anything is unclear please hover your mouse over the superscripts! ((Because they might just give you some addiotional hints ;-))) For the most part we will be assuming you have at least a little familiarity with Linux. Much of this information is available elsewhere in the CHPC's wiki (probably in more detail), but here we are trying to have everything accessible in one place for the bioinformatics community. Please do read the [[quick:start|quick start guide]] before continuing and pay special attention to the sections on [[quick:start#queues|queues]] and [[quick:start#job_script_parameters|parameters]]((especially the -P parameter)).
+The CHPC has a Globus endpoint: Look for **CHPC-Lengau** to transfer data to/from the cluster storage. Access it via http://globus.org/ and your cluster username/password.
 ===== Web Portal Access =====
-Web-based access to the CHPC cluster is available via a //Galaxy//(([[http://galaxyproject.org/]])) web interface at [[http://galaxy.chpc.ac.za/]]. Another workflow-based system uses //chipster//(([[http://chipster.csc.fi/|chipster website]])) but
+Galaxy GUI access to the cluster has been provided in the past and may be made available in the future
-uses a dedicated VM and does not run on the cluster [[http://chipster.chpc.ac.za/]].
+if there is enough demand for it from our users.
 To transfer files inward using gridftp, the [[http://globus.org/]] system can be used,
-and is accessible via our endpoint named ''chpcbio#globus.chpc.ac.za''. You should
+and is accessible via our endpoint named ''CHPC-Lengau''. You should
 use the same credentials used to log in via ssh.
 ===== Command Line Access =====
-Various opensource packages have been pre-installed at the CHPC. For the moment they're on the SUN cluster but where appropriate they will be ported to the other architectures. First one must [[http://www.chpc.ac.za/index.php/contact-us/apply-for-resources-form|apply for resources]] to gain access to the cluster. Once your registration has been approved then Linux and OSX users can simply open a terminal and connect via ssh to the server using a command of the form((Note that //**localuser@my_linux:~ $**// is not part of the command)):
+Before one gains access to the command line, you should have an account. In order to get an account you and your PI should both follow the instructions to [[https://users.chpc.ac.za/procedures/|apply for resources]].
-<code bash>localuser@my_linux:~ $ ssh username@sun.chpc.ac.za
-Last login: Tue Jan 28 14:05:35 2014 from 10.128.23.235
+Once your registration has been approved then Linux and OSX users can simply open a terminal and connect via ssh to the server using a command of the form((Note that //**localuser@my_linux:~ $**// is not part of the command)):
-username@login01:~ $</code>
+<code bash>localuser@my_linux:~ $ ssh username@lengau.chpc.ac.za
-where //user// is the username you are assigned upon registration. Windows users can [[http://www.chiark.greenend.org.uk/~sgtatham/putty/download.html|download the putty client]] ((Here is the [[http://the.earth.li/~sgtatham/putty/0.63/htmldoc/Chapter2.html#gs|getting started with putty]] guide)). Once connected users can: [[howto:bioinformatics#Using Modules|use the modules system]] to get access to bioinformatics programs; [[howto:bioinformatics#Create Job Scripts|create job scripts]] using editors such as //vim//(([[http://vimdoc.sourceforge.net/htmldoc/usr_02.html|vim user guide]])) or //nano//(([[http://www.nano-editor.org/dist/v2.0/nano.html|nano user guide]])); and finally [[howto:bioinformatics#Submit Job Script| submit]] and [[howto:bioinformatics#Monitor jobs|monitor]] their jobs.
+Last login: Mon Feb 29 14:05:35 2016 from 10.128.23.235
+username@login1:~ $</code>
+where //user// is the username you are assigned upon registration. Windows users can [[http://www.chiark.greenend.org.uk/~sgtatham/putty/download.html|download the putty client]] ((Here is the [[http://the.earth.li/~sgtatham/putty/0.63/htmldoc/Chapter2.html#gs|getting started with putty]] guide)).
+Once connected users can: [[howto:bioinformatics#Using Modules|use the modules system]] to get access to bioinformatics programs; [[howto:bioinformatics#Create Job Scripts|create job scripts]] using editors such as //vim//(([[http://vimdoc.sourceforge.net/htmldoc/usr_02.html|vim user guide]])) or //nano//(([[http://www.nano-editor.org/dist/v2.0/nano.html|nano user guide]])); and finally [[howto:bioinformatics#Submit Job Script| submit]] and [[howto:bioinformatics#Monitor jobs|monitor]] their jobs.
 ==== Using Modules ====
-For now a quick and simple way of getting access to the bioinformatics software is using the //module// function. First of all one should ensure that:
+For now a quick and simple way of getting access to the bioinformatics software is using the //module// function. Running:<code bash>username@login2:~ $ module avail</code> will present you with the various modules available on the system and you should see something like:
-<code bash>export MODULEPATH=/opt/gridware/bioinformatics/modules:$MODULEPATH</code>
-exists in your **//~/.profile//** file((it is not included by default)). Then running:<code bash>username@login01:~ $ module avail</code> will present you with the various modules available on the system and you should see something like:
 <file>
------------------------- /opt/gridware/bioinformatics/modules -------------------------
+------------------------------------------------ /cm/local/modulefiles ------------------------------------------------
-R/2.15.2                    bowtie/0.12.9               gcc_4.7.2_libs
+cluster-tools/7.1         freeipmi/1.4.8            mvapich2/mlnx/gcc/64/2.1  use.own
-R/2.15.3                    bowtie/1.0.0                lam/7.1.4
+cluster-tools-dell/7.1    gcc/5.1.0                 null                      version
-R/3.0.0                     bowtie2/2.1.0               latex/texlive_2012
+cmd                       ipmitool/1.8.15           openldap
-R/default                   clustal/clustal-omega-1.1.0 mpich2/1.5
+cmsh                      module-git                openmpi/mlnx/gcc/64/1.8.8
-beagle/beagle_lib-r1090     clustal/clustalw-2.1        perl/5.16.3
+dot                       module-info               shared
-beagle/default              clustal/clustalw-MPI-1.82   python/2.7.3
-beast/beast-1.7.2           cufflinks/2.0.2             samtools/0.1.18
-beast/default               cufflinks/2.1.1             tophat/2.0.8b
-bioperl/1.6.1               emboss/6.5.7                velvet/1.2.08
-------------------- /opt/gridware/modules-3.2.7/Modules/3.2.7/CHPC --------------------
+----------------------------------------------- /cm/shared/modulefiles ------------------------------------------------
-amber/12(default)               intel2012
+acml/gcc/64/5.3.1                            chpc/python/anaconda/2
-clustertools                    inteltools
+acml/gcc/fma4/5.3.1                          chpc/python/anaconda/3
-dell/default-environment        mvapich2/1.8-gnu
+acml/gcc/mp/64/5.3.1                         chpc/qespresso/5.3.0/openmpi-1.8.8/gcc-5.1.0
-dell/moab                       mvapich2/1.8-r5668
+acml/gcc/mp/fma4/5.3.1                       chpc/R/3.2.3-gcc5.1.0
-dell/openmpi/intel/1.4.4        netcdf/gnu-4.1.2
+acml/gcc-int64/64/5.3.1                      chpc/vasp/5.3/openmpi-1.8.8/gcc-5.1.0
-dell/torque/2.5.12              netcdf/intel-4.1.2
+acml/gcc-int64/fma4/5.3.1                    chpc/zlib/1.2.8/intel/16.0.1
-dlpoly/2.20-impi                openfst/1.3.3-gnu
+acml/gcc-int64/mp/64/5.3.1                   cmgui/7.1
-dlpoly/2.20-steve-impi          openfst/1.3.3-intel
+acml/gcc-int64/mp/fma4/5.3.1                 default-environment
-dlpoly/3.07-impi                openmpi/openmpi-1.6.1-gnu
+acml/open64/64/5.3.1                         gdb/7.9
-dlpoly/3.09-iompi               openmpi/openmpi-1.6.1-gnu.bak
+acml/open64/fma4/5.3.1                       hdf5/1.6.10
-espresso/3.1.2                  openmpi/openmpi-1.6.1-intel
+acml/open64/mp/64/5.3.1                      hdf5_18/1.8.14
-fftw/3.3.2-intel                openmpi/openmpi-1.6.1-intel.bak
+acml/open64/mp/fma4/5.3.1                    hpl/2.1
-g09                             sapt/2008
+acml/open64-int64/64/5.3.1                   hwloc/1.9.1
-gcc/4.6.3                       sunstudio
+acml/open64-int64/fma4/5.3.1                 intel/compiler/64/15.0/2015.5.223
-gcc/4.7.2                       tau
+acml/open64-int64/mp/64/5.3.1                intel-cluster-checker/2.2.2
-intel                           zlib/1.2.7
+acml/open64-int64/mp/fma4/5.3.1              intel-cluster-runtime/ia32/3.7
+blas/gcc/64/3.5.0                            intel-cluster-runtime/intel64/3.7
+blas/open64/64/3.5.0                         intel-cluster-runtime/mic/3.7
+bonnie++/1.97.1                              intel-tbb-oss/ia32/43_20150424oss
+chpc/amber/12/openmpi-1.8.8/gcc-5.1.0        intel-tbb-oss/intel64/43_20150424oss
+chpc/amber/14/openmpi-1.8.8/gcc-5.1.0        iozone/3_430
+chpc/BIOMODULES                              iperf/3.0.11
+chpc/cp2k/2.6.2/openmpi-1.8.8/gcc-5.1.0      lapack/gcc/64/3.5.0
+...
 </file>
-Now to make use of, tophat say, one can type:<code bash>username@login01:~ $ module add tophat/2.0.8b</code>The appropriate environmental variables are set (usually as simple as adding a directory to the search path). Notice that often there are several versions of software available, e.g. **//R//** versions **//2.15.2//**, **//2.15.3//** and **//3.0.0//**. The module system then allows you to choose which version specifically you'd like to use by running a command such as **''module add R/2.15.3''**. **Note:** it is better in general to be specific about which version you'd like to use rather than assuming the system will know. Running:<code bash>username@login01:~ $ module list</code> will show which modules have been loaded. Whereas:<code bash>username@login01:~ $ module del modulename</code> will unload a module. And finally: <code bash>username@login01:~ $ module show modulename</code> will show what module //modulename// actually does.
+Bioinformatics modules are expected to add a lot to that list and so have a list of their own. Running <code bash>username@login2:~ $ module add chpc/BIOMODULES</code> followed by <code bash>username@login2:~ $ module avail</code> will result in the following being added to the above list (this should be much expanded as various applications are added to the system):
+<file>
+----------------------------------------- /apps/chpc/scripts/modules/bio/app ------------------------------------------
+anaconda/2             doxygen/1.8.11         java/1.8.0_73          ncbi-blast/2.3.0/intel R/3.2.3-gcc5.1.0
+anaconda/3             git/2.8.1              mpiblast/1.6.0         python/2.7.11          texlive/2015
+cmake/3.5.1            htop/2.0.1             ncbi-blast/2.3.0/gcc   python/3.5.1
+</file>
+Now to make use of, blast say, one can type:<code bash>username@login2:~ $ module add ncbi-blast/2.3.0/gcc</code>The appropriate environmental variables are set (usually as simple as adding a directory to the search path). Running:<code bash>username@login2:~ $ module list</code> will show which modules have been loaded. Whereas:<code bash>username@login2:~ $ module del modulename</code> will unload a module. And finally: <code bash>username@login2:~ $ module show modulename</code> will show what module //modulename// actually does.
 ==== Create Job Scripts ====
@@ Line 66: / Line 80: @@
 <file bash my_job.qsub>
 #!/bin/bash
-#PBS -l select=1:ncpus=12:jobtype=dell,place=excl
+#PBS -l select=1:ncpus=2
 #PBS -l walltime=10:00:00
-#PBS -q workq
+#PBS -q serial
-#PBS -V
+#PBS -P SHORTNAME
-#PBS -o /export/home/username/scratch5/NGS_data/stdout.txt
+#PBS -o /mnt/lustre/users/username/my_data/stdout.txt
-#PBS -e /export/home/username/scratch5/NGS_data/stderr.txt
+#PBS -e /mnt/lustre/users/username/my_data/stderr.txt
 #PBS -N TophatEcoli
 #PBS -M myemailaddress@someplace.com
 #PBS -m b
-source /etc/profile.d/modules.sh
+module add chpc/BIOMODULES
-MODULEPATH=/opt/gridware/bioinformatics/modules:${MODULEPATH}
+module add tophat/2.1.1
-module add tophat/2.0.9
 NP=`cat ${PBS_NODEFILE} | wc -l`
@@ Line 85: / Line 98: @@
 ARGS="--num-threads ${NP} someindex reads1 reads2 -o output_dir"
-cd /export/home/username/scratch5/NGS_data/
+cd /mnt/lustre/users/username/my_data
 ${EXE} ${ARGS}
 </file>
-Note that //username// should be your username... More details on the job script file can be found [[quick:pbspro|in our PBS quickstart guide]].
+Note that //username// should be your username and //SHORTNAME// should be your research programme's code. More details on the job script file can be found [[quick:start|in our PBS quickstart guide]].
 ==== Submit Job Script ====
 Finally submit your job using:
-<code bash>username@login01:~ $ qsub my_job.qsub
+<code bash>username@login2:~ $ qsub my_job.qsub
-.chpcmoab0
+.sched01
-username@login01:~ $</code>
+username@login2:~ $</code>
-where //13614@chpcmoab0// is the //jobID// that is returned.
+where //192757.sched01// is the //jobID// that is returned.
 ==== Monitor jobs ====
@@ Line 107: / Line 120: @@
 == check status of pending and running jobs ==
 <code bash>
-username@login01:~ $ qstat -u username
+username@login2:~ $ qstat -u username
-chpcmoab01:
+sched01:
                                                             Req'd  Req'd   Elap
 Job ID          Username Queue    Jobname    SessID NDS TSK Memory Time  S Time
 --------------- -------- -------- ---------- ------ --- --- ------ ----- - -----
-.chpcmoab0 username workq    TophatEcol 17546   1   12   --  01:00 R 00:00
+.sched01  username serial   TophatEcol     --   1  24    --  00:02 Q   --
-username@login01:~ $
+username@login2:~ $
 </code>
 == check status of particular job ==
 <code bash>
-username@login01:~ $ qstat -f 13614.chpcmoab01
+username@login2:~ $ qstat -f 192759.sched01
-Job Id: 13614.chpcmoab01
+Job Id: 192759.sched01
     Job_Name = TophatEcoli
-    Job_Owner = username@login01
+    Job_Owner = username@login2.cm.cluster
     resources_used.cpupercent = 0
     resources_used.cput = 00:00:00
-    resources_used.mem = 16796kb
+    resources_used.mem = 0kb
-    resources_used.ncpus = 12
+    resources_used.ncpus = 96
-    resources_used.vmem = 166064kb
+    resources_used.vmem = 0kb
-    resources_used.walltime = 00:02:32
+    resources_used.walltime = 00:00:00
     job_state = R
-    queue = workq
+    queue = serial
-    server = chpcmoab01
+    server = sched01
     Checkpoint = u
-    ctime = Tue Jan 28 13:15:41 2014
+    ctime = Mon Oct 10 06:57:13 2016
-    Error_Path = /export/home/username/scratch5/NGS_data/stderr.txt
+    Error_Path = login2.cm.cluster:/mnt/lustre/users/username/my_data/stderr.txt
-    exec_host = cnode-9-34/2*12
+    exec_host = cnode0962/0*24
-    exec_vnode = (cnode-9-34:ncpus=12)
+    exec_vnode = (cnode0962:ncpus=24)
     Hold_Types = n
-    interactive = True
     Join_Path = n
     Keep_Files = n
     Mail_Points = a
-    mtime = Tue Jan 28 13:15:42 2014
+    mtime = Mon Oct 10 06:57:15 2016
-    Output_Path = /export/home/username/scratch5/NGS_data/stdout.txt
+    Output_Path = login2.cm.cluster:/mnt/lustre/users/username/my_data/stdout.txt
     Priority = 0
-    qtime = Tue Jan 28 13:15:41 2014
+    qtime = Mon Oct 10 06:57:13 2016
-    Rerunable = False
+    Rerunable = True
-    Resource_List.ncpus = 12
+    Resource_List.ncpus = 24
     Resource_List.nodect = 1
     Resource_List.place = free
-    Resource_List.select = 1:ncpus=12:jobtype=dell
+    Resource_List.select = 1:ncpus=24
-    Resource_List.walltime = 20:00:00
+    Resource_List.walltime = 00:02:00
-    stime = Tue Jan 28 13:15:42 2014
+    stime = Mon Oct 10 06:57:15 2016
-    session_id = 16154
+    session_id = 36609
-    jobdir = /export/home/username/scratch5/NGS_data
+    jobdir = /mnt/lustre/users/username
     substate = 42
     Variable_List = PBS_O_SYSTEM=Linux,PBS_O_SHELL=/bin/bash,
-        PBS_O_HOME=/export/home/user,PBS_O_LOGNAME=username,
+        PBS_O_HOME=/home/dane,PBS_O_LOGNAME=username,PBS_O_WORKDIR=/mnt/lustre/users/username/my_data,
-        PBS_O_WORKDIR=/export/home/username/scratch5/NGS_data,
+        PBS_O_LANG=en_ZA.UTF-8,
-        PBS_O_LANG=en_US.UTF-8,
+        PBS_O_PATH=/apps/chpc/bio/anaconda3/bin:/apps/chpc/bio/R/3.3.1/gcc-6.2
-        PBS_O_PATH=/opt/gridware/bioinformatics/emacs/emacs-24.3/bin:/export/h
+        .0/bin:/apps/chpc/bio/bzip2/1.0.6/bin:/apps/chpc/bio/curl/7.50.0/bin:/a
-        ome/username/local/bin:/usr/lib64/qt-3.3/bin:/opt/pbs/default/sbin/:/op
+        pps/chpc/bio/lib/png/1.6.21/bin:/apps/chpc/bio/openmpi/2.0.0/gcc-6.2.0_
-        t/pbs/default/bin/:/usr/kerberos/bin:/usr/local/bin:/bin:/usr/bin,
+        java-1.8.0_73/bin:...
-        PBS_O_MAIL=/var/spool/mail/username,PBS_O_QUEUE=workq,
+    comment = Job run at Mon Oct 10 at 06:57 on (cnode0962:ncpus=24)+(cnode0966
-        PBS_O_HOST=login01
+        :ncpus=24)+(cnode0971:ncpus=24)+(cnode0983:ncpus=24)
-    comment = Job run at Tue Jan 28 at 13:15 on (cnode-9-34:ncpus=12)
+    etime = Mon Oct 10 06:57:13 2016
-    etime = Tue Jan 28 13:15:41 2014
+    umask = 22
-    Submit_arguments = -I -l select=1:ncpus=12:mpiprocs=12:jobtype=dell,
+    run_count = 1
-        place=free -N TophatEcoli -l walltime=20:00:00
+    eligible_time = 00:00:00
-    project = _pbs_project_default
+    Submit_arguments = my_job.qsub
+    pset = rack=cx14
+    project = SHORTNAME
 username@login01:~ $
@@ Line 175: / Line 190: @@
 == canceljob ==
 <code bash>
-username@login01:~ $ qdel 13614.chpcmoab01
+username@login01:~ $ qdel 192759.sched01
 username@login01:~ $
 </code>
-===== Basic examples =====
-==== Blast ====
+===== Software Environments =====
-=== Running Blast on the M9000 ===
+==== Conda ====
+Many scientific software tools rely on specific versions of libraries, compilers, and dependencies that often conflict with each other or with system-wide installations. **Conda** is a powerful, language-agnostic environment and package manager that helps solve this problem by allowing users to manage **Python**, **R**, **C/C++**, **FORTRAN**, and other language ecosystems in **isolated environments**.
-One thing to note is that one cannot use scratch on the m9000 -- so jobs must be run in the user's home (or a sub-directory of home).
+=== Shared Conda Environments ===
-== Job script ==
+For most use cases, especially in bioinformatics, CHPC provides pre-built, **shared Conda environments** installed under:
-Your job script will look something like this((Note you can click on the tab //my_job.qsub// to download this if you wish to use it as a template. Or you can just copy and paste...)):
-<file bash my_job.qsub>
-#! /bin/bash
-#PBS -l select=1:ncpus=128:mpiprocs=128:jobtype=spark
-#PBS -l place=free
-#PBS -l walltime=06:00:00
-#PBS -q spark
-#PBS -o /export/home/username/blastjob/stdout.txt
-#PBS -e /export/home/username/blastjob/stderr.txt
-#PBS -M youremail@address.com
-#PBS -m be
-#PBS -N m9000_blast
-# NOTE: The M9000 has its own scratch space separate from main Lustre storage
+  '/apps/chpc/bio/anaconda3-2020.02/envs'
-# So run in your home, or a subdir of home, or request via helpdesk that a
-# scratch directory be created for you on the m9000, eg. in ''/scratch/work/username''
-cd /export/home/username/blastjob
+These environments are curated by CHPC staff to include commonly used tools in genomics, transcriptomics, and other domains.
-NP=`cat $PBS_NODEFILE | wc -l`
-EXE="/opt/gridware/bioinformatics/m9000/ncbi-blast-2.2.24/bin/blastx"
+=== Step-by-step usage ===
-ARGS="-db /scratch/work/bioinfo/BLASTDB/nr -query my_seqs.fasta -evalue 0.001 -num_alignments 20 -outfmt 5 -num_threads ${NP} > my_results.xml"
-$EXE $ARGS
+=== Step 1: Load required modules ===
-</file>
+To access Conda functionality, first load the required modules:
+<code bash>
+module load chpc/BIOMODULES
+module load conda_init
+</code>
-Of course one should set the parameters as required. (Setting a small evalue is recommended as is limiting the number of alignments). For blast2go users remember to set //-outfmt// to //5// for XML output. Note one should also select the correct **//EXE//**cutable and **//-db//**: //blastx//, //blastn// and //blastp// are available for the former, while //nr// and //nt// are available for the latter.
+The second module updates your .bashrc file by adding necessary shell variables.
-== Submit your job ==
+To apply these changes, you can either log out and log back in, or run: <code bash>source ~/.bashrc. </code>
-Finally submit your job using:<code bash>user@login01:~ $ qsub my_job.qsub</code>
+After this setup, you won’t need to load additional modules for your jobs—only the eval and conda activate steps are required.
+=== Step 2: Initialize Conda in your shell ===
+Activate Conda shell integration:
+<code bash>
+eval "$(conda shell.bash hook)"
+</code>
+This command sets up your shell environment to recognize Conda commands like `conda activate`.
+=== Step 3: List available environments ===
+<code bash>
+conda info --envs
+</code>
+This will display all available shared Conda environments and their paths.
+=== Step 4: Activate a shared environment ===
+<code bash>
+conda activate nameOfTheEnv
+</code>
+Replace ''nameOfTheEnv'' with the name of an environment from the previous step.
+> **Tip:** If you're unsure which environment to use, contact CHPC support or explore the environment's contents with `conda list`.
+> **Note:** You do **not** need to install anything when using shared environments.
+=== Creating Private Conda Environments ===
+If you need software that is not included in the shared environments, you may create your own **private Conda environment**. This gives you full control over the software stack and package versions.
+> **Important:** Do **not** install environments in your home directory (''/home/<username>'') -use your Lustre project storage instead.
+=== Step-by-step setup ===
+ssh to username@scp.chpc.ac.za, the password is the same as the one you use on lengau
+=== Step 1: Load Conda ===
+<code bash>
+module load chpc/BIOMODULES
+module load conda_init
+eval "$(conda shell.bash hook)"
+</code>
+=== Step 2: Create a new environment ===
+<code bash>
+conda create --prefix /mnt/lustre/<username>/myenv python=3.10
+</code>
+This will create a Conda environment at the specified path with Python 3.10 installed. You can replace the Python version or leave it out if not needed.
+=== Step 3: Activate your environment ===
+<code bash>
+conda activate /mnt/lustre/<username>/myenv
+</code>
+After activation, you can install any packages you need.
+=== Step 4: (Optional) Install Mamba for faster package management ===
+<code bash>
+conda install mamba -n base -c conda-forge
+</code>
+> **Tip:** Mamba is a drop-in replacement for Conda that uses a faster dependency solver written in C++. Once installed, you can use `mamba` instead of `conda` for installing packages:
+<code bash>
+mamba install numpy pandas
+</code>
+This significantly speeds up installations and environment solves, especially when working with large scientific packages.
+=== Step 5: Install packages ===
+<code bash>
+conda install numpy pandas matplotlib
+</code>
+You can install packages one by one, or include them during environment creation:
+<code bash>
+conda create --prefix /mnt/lustre/<username>/myenv python=3.10 numpy pandas
+</code>
+=== Step 6: Remove unused environments ===
+Old or unused environments can be removed to free up space:
+<code bash>
+conda remove --prefix /mnt/lustre/<username>/myenv --all
+</code>
+=== Best Practices ===
+  * ✅ Use **shared environments** whenever possible for consistency and faster setup.
+  * 📁 Create private environments **only in Lustre** directories, such as ''/mnt/lustre/<username>''.
+  * ⚠️ Do **not** use Conda in your ''$HOME'' directory, it may lead to quota issues or slow performance.
+  * 📌 Use the ''--prefix'' flag to create environments with absolute paths, especially on clusters where ''--name'' may default to ''$HOME''.
+  * 🧼 Periodically clean up unused environments with `conda remove --all`.
+  * 🔁 Reuse environment definitions by exporting and sharing them with others or for reproducibility.
+=== Troubleshooting ===
+  * ❓ **Conda not recognized?** Make sure you loaded `conda_init` and ran `eval "$(conda shell.bash hook)"`.
+  * 🚫 **Permission denied?** You might be trying to write to a restricted directory like ''/apps'' or ''$HOME''.
+  * 🔄 **Environment behaving unexpectedly?** Try deactivating (`conda deactivate`) and reactivating, or recreate the environment.
+  * 🧪 **Conflicts during install?** Use `conda clean --all` to clear caches and retry with a minimal environment.
+==== Singularity ====
+Singularity is an open-source, cross-platform container platform specifically designed for scientific and high-performance computing environments. It prioritizes reproducibility, portability, and security, all essential for scientific workflows. Singularity enables users to package entire workflows, including software, libraries, and environment settings, into a single container image. This ensures consistent application execution across various systems without modification. This capability simplifies the migration of complex computational environments and supports reproducible research practices. [[https://docs.sylabs.io/guides/3.7/user-guide/|A detailed Singularity user guide is available here]].
+=== Location of Bioinformatics Singularity Images at CHPC ===
+Singularity images for commonly used bioinformatics tools are stored in the following directories:
+<code>
+/apps/chpc/bio
+/home/apps/chpc/bio
+</code>
+To view the available .sif images, run the following script:
+<code bash>
+#!/bin/bash
+dirs=("/home/apps/chpc/bio" "/apps/chpc/bio")
+# Loop through and search for .sif files only in immediate subdirectories
+for dir in "${dirs[@]}"; do
+    if [ -d "$dir" ]; then
+        echo "Searching for .sif files under $dir (only first subfolder level):"
+        find "$dir" -mindepth 2 -maxdepth 2 -type f -name "*.sif" -readable -exec ls -al {} \; 2>/dev/null
+    else
+        echo "Directory $dir does not exist."
+    fi
+done
+</code>
+=== Pulling a Singularity Image ===
+Before pulling a new image, run the script above to check if it’s not already available. Only proceed with pulling the image yourself if you’re confident in what you’re doing and plan to remove it afterwards.
+⚠️ **Important**: Singularity image files can be very large and may consume significant storage in your Lustre or project directory. Please remove any images you no longer need to help conserve shared storage resources.
+**To pull Singularity images from public container registries (like DockerHub), follow these steps:**
+SSH into the CHPC Globus node:
+<code bash>
+ssh username@globus.chpc.ac.za
+</code>
+Load the Singularity module:
+<code bash>
+module load chpc/singularity
+</code>
+Navigate to your desired working directory:
+<code bash>
+cd /path/to/working_directory
+</code>
+Pull the image from DockerHub (or another registry):
+<code bash>
+singularity pull docker://repository/image:tag
+</code>
+This downloads and converts the image into a local .sif file saved in your current directory.
+===Running Singularity===
+<code bash>
+singularity exec /path/to/image.sif <command> <OPTIONS>
+</code>
+=== Running Singularity with External Databases ===
+Most bioinformatics containers don’t include large reference datasets. Instead, bind external directories at runtime.
+CHPC provides bioinformatics databases at:
+<code>
+/mnt/lustre/bsp/DB
+</code>
+These include reference genomes, annotation and index files used by BWA, BLAST, Kraken2, etc.
+** How to Bind a Database Directory **
+Use the --bind (or -B) option:
+<code bash>
+singularity exec --bind /mnt/lustre/bsp/DB:/databases /path/to/my_image.sif <your_command>
+</code>
+**Explanation**:
+/mnt/lustre/bsp/DB:/databases → Host path mapped to container path
+/path/to/my_image.sif → Singularity image path
+<your_command> → The tool command (e.g., bwa index, blastn, etc.)
+Inside the container, always refer to the database as /databases unless specified otherwise on the manual.
+== Binding Multiple Directories ==
+Use a comma-separated list:
+<code bash>
+singularity exec --bind /mnt/lustre/bsp/DB:/databases,/mnt/lustre/username/data:/data /path/to/my_image.sif <your_command>
+</code>
+This binds:
+- /mnt/lustre/bsp/DB to /databases
+- /mnt/lustre/username/data to /data
+Use those paths in your tools or pipelines.
+**Best Practices**
+. Use absolute paths for bindings.
+. Keep host/container paths logical (e.g., /databases, /data).
+. Clean up containers and intermediate data regularly.
+To clean up:
+<code bash>
+rm /path/to/image.sif
+rm -rf /path/to/working_directory/*.sif
+</code>
+**Clean the Singularity cache periodically:**
+<code bash>
+singularity cache clean
+</code>
+=== PBS Template for Running a Singularity Container ===
+<code bash>
+#!/bin/bash
+#PBS -N singularity_job
+#PBS -q normal
+#PBS -l select=1:ncpus=24
+#PBS -l walltime=12:00:00
+#PBS -o singularity_output.log
+#PBS -e singularity_error.log
+#PBS -M your.email@domain.com
+#PBS -m abe
+# Load necessary modules
+module load chpc/singularity
+# Change to your working directory
+cd $PBS_O_WORKDIR
+# Run your command inside the container
+singularity exec --bind /mnt/lustre/projects/<your_project>:/data my_image.sif <your_command_inside_container>
+</code>
+==== Nextflow ====
+Nextflow is a free and open-source workflow management system that enables the development and execution of data analysis pipelines. It simplifies complex computational workflows and ensures reproducibility, scalability, and portability—whether you’re working on a laptop, HPC cluster, or in the cloud. Nextflow workflows are written using DSL2, allowing modular code design and seamless integration with container technologies like Docker, Singularity, Conda, or manual installations.
+[[https://www.nextflow.io/docs/latest/index.html|Official documentation is available here]].
+=== Running Nextflow on the CHPC Cluster ===
+CHPC supports Nextflow workflows through Singularity containers. Since compute nodes have no internet access, all dependencies must be downloaded in advance on the login node.
+=== 1. Connect to the Login Node ===
+Log into the CHPC login node using your Lengau credentials:
+<code bash> ssh username@scp.chpc.ac.za </code>
+Use this session to prepare your workflow and submit jobs.
+=== 2. Load the Nextflow Module ===
+Load the necessary environment modules:
+<code bash>module load chpc/BIOMODULES nextflow
+module load chpc/singularity
+</code>
+Note: Modules must be reloaded in every new session unless added to your ~/.bashrc.
+=== 3. Pull Workflow and Dependencies ===
+Pull your workflow and dependencies on the login1 node:
+Pull the workflow:
+<code bash> nextflow pull nf-core/rnaseq </code>
+Run a test execution:
+<code bash> nextflow run nf-core/rnaseq -profile test </code>
+This will:
+Cache the workflow in ~/.nextflow/assets/
+Download containers (if configured)
+Retrieve auxiliary files and dependencies
+=== Cached Files and Workflow Structure ===
+Workflow code is stored in:
+<code>~/.nextflow/assets</code>
+Container images are stored in:
+<code>~/.singularity</code>
+**🗂 Finding the nextflow.config File**
+After pulling a workflow, you’ll typically find the nextflow.config file in its root directory.
+Example:
+<code bash>
+cd ~/.nextflow/assets/nf-core/rnaseq/
+ls
+</code>
+Look for:
+<code>nextflow.config</code>
+If missing, config files may reside in the conf/ directory or be fetched remotely. You can always override settings by creating your own nextflow.config.
+🚫 No Manual PBS Scripts Needed
+Nextflow automatically generates and submits PBS scripts. You only define resources in nextflow.config.
+=== ⚙️ Configuration with nextflow.config ===
+== 🔧 1. Global Resource Settings ==
+Set default resource usage for all workflow processes:
+<code nextflow> process {
+    executor = 'pbs'
+    withLabel: big_job {
+        queue = 'smp'
+        cpus = 24
+        memory = '120 GB'
+        time = '24h'
+    }
+}
+ </code>
+== 🏷️ 2. Custom Resource Labels ==
+Customize resources for specific process groups using labels:
+<code nextflow>
+process {
+    executor = 'pbs'
+    withLabel: big_job {
+        cpus = 16
+        memory = '64 GB'
+        time = '12h'
+        queue = 'smp'
+    }
+    withLabel: short_job {
+        cpus = 1
+        memory = '1 GB'
+        time = '15m'
+        queue = 'smp'
+    }
+}
+</code>
+Use the label in your pipeline:
+<code nextflow>
+process bigTask {
+label 'big_job'
+...
+}
+</code>
+== 📦 3. Singularity Integration ==
+Enable Singularity support:
+<code nextflow> singularity.enabled = true
+singularity.autoMounts = true </code>
+Specify containers:
+From Docker Hub:
+<code nextflow>
+process.container = 'docker://biocontainers/fastqc:v0.11.9_cv8'
+</code>
+From local image:
+<code nextflow>
+process.container = '/path/to/image.sif'
+</code>
+Set cache directory to avoid re-downloads:
+<code nextflow> singularity.cacheDir = '/path/to/.singularity' </code>
+== 🖥️ 4. PBS Executor Settings ==
+Customize PBS job submission:
+<code nextflow>
+executor {
+  name = 'pbs'
+  queueSize = 20
+  submitOptions = '-V -m abe -M your@email.com'
+}
+</code>
+== 📂 5. Using Profiles ==
+Profiles let you switch configurations easily:
+<code nextflow> profiles {
+  standard {
+    process.executor = 'pbs'
+    process.queue = 'smp'
+  }
+  local {
+    process.executor = 'local'
+    docker.enabled = false
+  }
+  cluster_singularity {
+    process.executor = 'pbs'
+    singularity.enabled = true
+    process.container = 'file:///path/to/container.sif'
+  }
+}
+ </code>
+Run a profile:
+<code bash> nextflow run main.nf -profile cluster_singularity </code>
+== 🚫 Offline Mode ==
+Run jobs on compute nodes without internet access:
+<code bash> nextflow run ~/.nextflow/assets/nf-core/rnaseq \
+-profile singularity -offline </code>
+⚠️ Always include -offline on compute nodes to prevent online fetching.
+=== 🧭 Debugging and Logs ===
+Each Nextflow process generates a unique work directory (work/ab/xyz123), containing:
+.command.run — generated PBS job script
+.command.sh — wrapped shell script
+.command.log — job output
+.exitcode — exit status
+To inspect a failed job:
+<code bash> cd work/ab/xyz123/
+less .command.log </code>
+=== ✅ Summary ===
+nextflow.config centralizes all pipeline settings.
+No need to write PBS scripts manually.
+Resources, container usage, and submission options are all configurable.
+Profiles improve portability and reproducibility.
+Offline mode is essential for CHPC compute node compatibility.
+🧠 Tip: For workflows requiring reference data, bind directories just like with containers:
+<code bash> nextflow run /path/to/my_pipeline -profile singularity -offline \
+--input /data/input.fastq \
+--genomeDir /mnt/lustre/bsp/DB/genomes
+</code>
+🧹 Clean Up:
+Nextflow stores all its cache files in your home directory, so it's important to clean up these files once you're finished using a workflow to avoid running out of space.
+<code bash>
+rm -rf ~/.nextflow/assets/
+rm -rf ~/.nextflow/tmp
+rm -rf ~/.singularity
+</code>
+=== Need Help? ===
+If you encounter issues or need a specific tool installed contact the CHPC support team at:
+  * 📧 help@chpc.ac.za
+  * https://users.chpc.ac.za/helpdesk/tickets/submit/
+Include your job script and all errors encountered.
+===== Basic examples =====
+==== Blast ====
+=== Running Blast using gnu parallel ===
+Several examples of running blast can be found in this page of using [[howto:bioinformatics:gnu-parallel#fault_tolerant_blast|fault tolerant blast]].
 === Running Blast on sun cluster ===
@@ Line 222: / Line 728: @@
 <file bash sun_blast.sh>
 #!/bin/bash
-WORKDIR="/export/home/${USER}/scratch5/blast_proj"
+WORKDIR="/lustre/users/${USER}/blast_proj"
 INPUT_FASTA=${WORKDIR}/data_set.fa.gz
 BLAST_E_VAL="1e-3"
-BLAST_DB="/lustre/SCRATCH5/groups/bioinfo/DBs/BLAST/nr"
+BLAST_DB="/mnt/lustre/bsp/NCBI/BLAST/nr"
-JOBTYPE=nehalem
+THREADS=24
-THREADS=8
 BLAST_HOURS=0
 BLAST_MINUTES=30
@@ Line 243: / Line 748: @@
 TMPSCRIPT=thejob.sh
 # note: make a distinction between variables set by the containing script (e.g. WORKDIR) and
 # ones set in the script (e.g. INDEX). The ones set in the script need to be escaped out
 cat >${TMPSCRIPT} << END
 #!/bin/bash
+#PBS -l select=1:ncpus=${THREADS}
-#PBS -l select=1:ncpus=${THREADS}:jobtype=${JOBTYPE}
+#PBS -l place=excl:group=nodetype
-#PBS -l place=excl:group=nodetype
+#PBS -l walltime=${BLAST_HOURS}:${BLAST_MINUTES}:00
-#PBS -l walltime=${BLAST_HOURS}:${BLAST_MINUTES}:00
+#PBS -q normal
-#PBS -q workq
+#PBS -m ae
-#PBS -m ae
+#PBS -M ${MAIL_ADDRESS}
-#PBS -M ${MAIL_ADDRESS}
+. /etc/profile.d/modules.sh
-. /etc/profile.d/modules.sh
+module add chpc/BIOMODULES
-module add blast/2.2.29+
+module add ncbi-blast/2.6.0
 INDEX="${WORKDIR}/${SPLIT_PREFIX}\${PBS_ARRAY_INDEX}"
 INFILE="\${INDEX}.split.fasta"
 OUTFILE="\${INDEX}.blastx.xml"
 cd ${WORKDIR}
-blastx -num_threads 8 -evalue ${BLAST_E_VAL} -db ${BLAST_DB} -outfmt 5 -query \${INFILE} -out \${OUTFILE}
+blastx -num_threads 8 -evalue ${BLAST_E_VAL} -db ${BLAST_DB} -outfmt 5 -query \${INFILE} -out \${OUTFILE} END
-END
 BLAST_JOBID=$(qsub -N sunblast -J ${START}-${END} ${TMPSCRIPT} | cut -d. -f1)
@@ Line 271: / Line 775: @@
 rm ${TMPSCRIPT}
 cat >${TMPSCRIPT} << END
 #!/bin/bash
+#PBS -l select=1:ncpus=1
-#PBS -l select=1:ncpus=1:jobtype=${JOBTYPE}
+#PBS -l place=free
-#PBS -l place=free:group=nodetype
+#PBS -l walltime=1:00:00
-#PBS -l walltime=1:00:00
+#PBS -q workq
-#PBS -q workq
+#PBS -m ae
-#PBS -m ae
+#PBS -M ${MAIL_ADDRESS}
-#PBS -M ${MAIL_ADDRESS}
+#PBS -W depend=afterok:${BLAST_JOBID}
-#PBS -W depend=afterok:${BLAST_JOBID}
+cd ${WORKDIR}
-cd ${WORKDIR}
+tar jcf blast-xml-output.tar.bz2 *.blastx.xml
-tar jcf blast-xml-output.tar.bz2 *.blastx.xml
+END
-END
 qsub -N tarblast ${TMPSCRIPT}
@@ Line 300: / Line 803: @@
     * Another important aspect of the job array is that the //walltime// parameter is the longest time you'd expect the sub-jobs to run in. So in this case we've divided a fasta file into many smaller faster files -- one for each sequence. In the event that your original sequences have widely differing lengths it may pay to have a different approach to the division -- perhaps one that results in the sub-fastas having similar sizes.
   - The use of job dependencies. We see it in the second //heredoc// in the line "//#PBS -W depend=afterok:${BLAST_JOBID}//". What this line does is that it says the job script only runs after the job with ID ${BLAST_JOBID} has successfully finished running, i.e. this job will not run if there are problems with the first job.
-==== Blast2Go ====
-A local instance of blast2go is available at the CHPC. It is accessible from outside the CHPC, however it does require you to set up some port forwarding.
-=== Port Forwarding ===
-This is accomplished via setting up port forwarding in your SSH session. In windows this is usually done in PuTTY, and in unix/osx this is done on the command line. **Note: This connection must stay on for as long as you wish to use CHPC's blast2go database.**
-== PuTTY ==
-When setting up the ssh connection you should go to: //connection -> SSH -> Tunnels//. Then add **3306** for //Source port// and **10.128.15.90:3306** for //Destination//. Then click //Add//.
-{{ :howto:bioinformatics:puttyconfigurationsshportforwarding.png?500 |}}
-You should then save your session (so that you don't have to fill this information in every time) and connect (using your normal CHPC login details).
-{{ :howto:bioinformatics:puttyconfigurationsession.png?500 |}}
-== SSH ==
-Your normal ssh command will change to look more like this:
-<code bash>localuser@my_linux:~ $ ssh username@sun.chpc.ac.za -L 3306:10.128.15.90:3306
-Last login: Tue Jan 28 14:05:35 2014 from 10.128.23.235
-username@login01:~ $</code>
-=== blast2go Configuration ===
-First you should go to the [[http://www.blast2go.com/b2ghome|blast2go website]] and start blast2go as normal by clicking on the **please click here** link((You may want to change the memory specifications here if you have lots of sequences)).
-{{ :howto:bioinformatics:blast2gowebstart.png?600 |}}
-A small file will download and you should then run it, and then blast2go proceeds to download the rest of the application.
-{{ :howto:bioinformatics:blast2godownloading.png?300 |}}
-Once blast2go is running go to: //Tools -> General Settings -> DataAccess Settings//.
-{{ :howto:bioinformatics:blast2goinitialsetup.png?600 |}}
-Then set:
-  * **Own Database**
-  * //DB Name//: **b2gdbFeb2014**
-  * //DB Host//: **localhost**
-  * //DB User//: **b2guser**
-  * //DB Password//: **blast4it**
-{{ :howto:bioinformatics:blast2godataaccessconfiguration.png?600 |}}
-and click //OK//.
-Then you will see in the bottom window/tab that it has connected to the database ((Open database connection to database 'b2gdbFeb2014' on 'localhost' as 'b2guser', with...)), and should also confirmed right at the bottom in the status message((Connected to own database: localhost: b2gdbFeb2014)).
-{{ :howto:bioinformatics:blast2godataaccessconfigurationdone.png?600 |}}
-Finally you may test the everything is working as expected by clicking on the white arrow in the green circle and confirm that you get the GO graph.
-{{ :howto:bioinformatics:blast2gotest.png?600 |}}
-==== Gromacs ====
-If you would like to try running gromacs on the gpu please take a look at [[howto:gpu_gromacs|this]].
-The job script that follows is for running an MPI compiled version of gromacs 4.6.1 on nehalem. There are many different versions of gromacs, to see what's available try:<code bash>user@login01:~ $ module avail</code>
-The following example is for working with one of the "_nehalem" gromacs modules -- note it's quite important to use the correct version as the input data changes with versions...
-=== Job script ===
-<file bash gromacs_nehalem.qsub>
-#!/bin/bash
-#PBS -l select=10:ncpus=8:mpiprocs=8:jobtype=nehalem,place=excl
-#PBS -l walltime=00:40:00
-#PBS -q workq
-#PBS -M user@someinstitution.ac.za
-#PBS -m be
-#PBS -V
-#PBS -e /export/home/user/scratch5/gromacs_data/std_err.txt
-#PBS -o /export/home/user/scratch5/gromacs_data/std_out.txt
-#PBS -N GROMACS_JOB
-#PBS -mb
-MODULEPATH=/opt/gridware/bioinformatics/modules:$MODULEPATH
-source /etc/profile.d/modules.sh
-#######module add
-module add gromacs/4.6.1_nehalem
-OMP_NUM_THREADS=1
-NP=`cat ${PBS_NODEFILE} | wc -l`
-EXE="mdrun_mpi"
-ARGS="-s XXX -deffnm YYYY"
-cd /export/home/user/scratch5/gromacs_data
-mpirun -np ${NP} -machinefile ${PBS_NODEFILE} ${EXE} ${ARGS}
-</file>
-=== Submit your job ===
-Finally submit your job using:<code bash>user@login01:~ $ qsub gromacs_nehalem.qsub</code>
 ==== bowtie ====
@@ Line 386: / Line 809: @@
 === Job script ===
-Then your job script called //gromacs_nehalem.qsub// will look something like this:
+Then your job script called //bowtie_script.qsub// will look something like this:
 <file bash bowtie_script.qsub>
 #! /bin/bash
-#PBS -l select=1:ncpus=12
+#PBS -l select=1:ncpus=24
 #PBS -l place=excl
 #PBS -l walltime=06:00:00
 #PBS -q workq
-#PBS -o /export/home/username/scratch5/some_reads/stdout.txt
+#PBS -o /home/username/lustre/some_reads/stdout.txt
-#PBS -e /export/home/username/scratch5/some_reads/stderr.txt
+#PBS -e /home/username/lustre/some_reads/stderr.txt
 #PBS -M youremail@address.com
 #PBS -m be
@@ Line 435: / Line 858: @@
 #PBS -l walltime=00:05:00
 #PBS -q workq
-#PBS -o /export/home/username/scratch5/namd2/stdout.txt
+#PBS -o /home/username/lustre/namd2/stdout.txt
-#PBS -e /export/home/username/scratch5/namd2/stderr.txt
+#PBS -e /home/username/lustre/namd2/stderr.txt
 #PBS -m ae
 #PBS -M youremail@address.com
@@ Line 452: / Line 875: @@
 === Submit your job ===
 Finally submit your job using:<code bash>user@login01:~ $ qsub namd.qsub</code>
-==== bowtie ====
-Things to note about this script -- bowtie currently does not run across multiple nodes. So using anything other than //select=1// will result in compute resources being wasted((Both because it will only run on a single node, and telling a process to use more threads than it has cores //usually// results in inefficiencies.)).
-=== Job script ===
-Then your job script called //gromacs_nehalem.qsub// will look something like this:
-<file bash bowtie_script.qsub>
-#! /bin/bash
-#PBS -l select=1:ncpus=12
-#PBS -l place=excl
-#PBS -l walltime=06:00:00
-#PBS -q workq
-#PBS -o /lustre/SCRATCH5/users/username/some_reads/stdout.txt
-#PBS -e /lustre/SCRATCH5/users/username/some_reads/stderr.txt
-#PBS -M youremail@address.com
-#PBS -m be
-#PBS -N bowtiejob
-##################
-MODULEPATH=/opt/gridware/bioinformatics/modules:$MODULEPATH
-source /etc/profile.d/modules.sh
-#######module add
-module add bowtie2/2.2.2
-NP=`cat ${PBS_NODEFILE} | wc -l`
-EXE="bowtie2"
-forward_reads="A_reads1.fq,B_reads_1.fq"
-reverse_reads="A_reads1.fq,B_reads_1.fq"
-output_file="piggy_hits.sam"
-ARGS="sscrofa --shmem --threads ${NP} --sam -q -1 ${forward_reads} -2 ${reverse_reads} ${output_file}"
-cd /lustre/SCRATCH5/users/username/some_reads
-${EXE} ${ARGS}
-</file>
-Note: username should contain your actual user name!
-=== Submit your job ===
-Finally submit your job using:<code bash>user@login01:~ $ qsub bowtie_script.qsub</code>
 ==== R/bioconductor ====
-=== pbdR example ===
+There is an example here on how one might use R on Lengau
-== Job scripts ==
-<file bash pbdtest.qsub>
-#PBS -l select=2:ncpus=8:mpiprocs=8:jobtype=nehalem,place=excl
-#PBS -l walltime=00:01:00
-#PBS -q workq
-#PBS -M YOUREMAILADDRESS
-#PBS -m be
-#PBS -V
-#PBS -e /lustre/SCRATCH5/users/USERNAME/pbdR_test/std_err.txt
-#PBS -o /lustre/SCRATCH5/users/USERNAME/pbdR_test/std_out.txt
-#PBS -N PBDR_TEST
-#PBS -mb
-MODULEPATH=/opt/gridware/bioinformatics/modules:$MODULEPATH
+http://wiki.chpc.ac.za/howto:r#r_bioconductor
-source /etc/profile.d/modules.sh
-module add R/3.2.0
-NP=`cat ${PBS_NODEFILE} | wc -l`
-cd /lustre/SCRATCH5/users/USERNAME/pbdR_test/
-mpirun -np ${NP} -machinefile ${PBS_NODEFILE} Rscript test_script.R
-</file>
-Note: __USERNAME__ should contain your actual user name!
-<file R test_script.R>
-library(pbdMPI, quiet=TRUE)
-init()
-my.rank <- comm.rank()
-comm.print(my.rank, all.rank=TRUE)
-finalize()
-</file>
-== Submit your job ==
-Finally submit your job using:<code bash>user@login01:~ $ qsub pbdtest.qsub</code>
 ==== tophat ====
@@ Line 551: / Line 899: @@
 ===== Databases =====
-Databases are accessible on the cluster in the <code bash>/lustre/SCRATCH5/groups/bioinfo/DBs</code> directory. Alternatively they are also mirrored on the [[http://bio.chpc.ac.za/data/|bio]] machine.
+Databases are accessible on the cluster in the  directory <code bash>/mnt/lustre/bsp/DB</code>
 ===== Support =====
-Please [[http://www.chpc.ac.za/index.php/support-resources/log-a-support-query|contact us]] to: request software updates/installs; download big datasets; get advice on the best way to run your analysis; or to tell us what is/isn't working!
+Please [[https://users.chpc.ac.za/helpdesk/tickets/submit |contact us]] to request software updates/installs; download big datasets; get advice on the best way to run your analysis; or to tell us what is/isn't working!

wiki.chpc.ac.za

User Tools

Site Tools

Differences

Page Tools