Difference between revisions of "TraCeR"

Latest revision as of 16:40, 22 August 2022

Description

This tool reconstructs the sequences of rearranged and expressed T cell receptor genes from single-cell RNA-seq data. It then uses the TCR sequences to identify cells that have the same receptor sequences and so derive from the same original clonally-expanded cell.

Environment Modules

Run module spider tracer to find out what environment modules are available for this application.

System Variables

HPC_TRACER_DIR - installation directory

Additional Information

To copy and use your own tracer config file use $ cp $HPC_TRACER_DIR/tracer.conf .

@@ Line 1: / Line 1: @@
-[[Category:Software]][[Category:Biology]][[Category:Biology]]
+[[Category:Software]][[Category:Biology]][[Category:Phylogenetics]]
 {|<!--CONFIGURATION: REQUIRED-->
 |{{#vardefine:app|tracer}}
@@ Line 5: / Line 5: @@
 <!--CONFIGURATION: OPTIONAL (|1}} means it's ON)-->
 |{{#vardefine:conf|}}           <!--CONFIGURATION-->
-|{{#vardefine:exe|}}            <!--ADDITIONAL INFO-->
+|{{#vardefine:exe|1}}            <!--ADDITIONAL INFO-->
 |{{#vardefine:pbs|}}            <!--PBS SCRIPTS-->
 |{{#vardefine:policy|}}         <!--POLICY-->
@@ Line 21: / Line 21: @@
 <!--Modules-->
-==Required Modules==
+==Environment Modules==
+Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
-===Serial===
-* {{#var:app}}
-<!--
-===Parallel (OpenMP)===
-* intel
-* {{#var:app}}
-===Parallel (MPI)===
-* intel
-* openmpi
-* {{#var:app}}
--->
 ==System Variables==
-* HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory
+* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 <!--Configuration-->
 {{#if: {{#var: conf}}|==Configuration==
@@ Line 43: / Line 32: @@
 {{#if: {{#var: exe}}|==Additional Information==
-WRITE_ADDITIONAL_INSTRUCTIONS_ON_RUNNING_THE_SOFTWARE_IF_NECESSARY
+To copy and use your own tracer config file use $ cp $HPC_TRACER_DIR/tracer.conf .
 |}}