Commit 67392217 authored by Leo Gordon's avatar Leo Gordon
Browse files

renamed the variable in the docs to match the code

parent fe00dfbc
......@@ -33,18 +33,18 @@ so it is best to install them under your home directory. For example,
It will be convenient to set a variable pointing at this directory for future use:
# using bash syntax:
$ export ENS_CODE_ROOT="$HOME/ensembl_main"
$ export ENSEMBL_CVS_ROOT_DIR="$HOME/ensembl_main"
#
# (for best results, append this line to your ~/.bashrc configuration file)
# using [t]csh syntax:
$ setenv ENS_CODE_ROOT "$HOME/ensembl_main"
$ setenv ENSEMBL_CVS_ROOT_DIR "$HOME/ensembl_main"
#
# (for best results, append this line to your ~/.cshrc or ~/.tcshrc configuration file)
2.2. Change into your ensembl codebase directory:
$ cd $ENS_CODE_ROOT
$ cd $ENSEMBL_CVS_ROOT_DIR
2.3. Log into the BioPerl CVS server (using "cvs" for password):
......@@ -75,18 +75,18 @@ It will be convenient to set a variable pointing at this directory for future us
2.8. Add new packages to the PERL5LIB variable:
# using bash syntax:
$ export PERL5LIB=${PERL5LIB}:${ENS_CODE_ROOT}/bioperl-live
$ export PERL5LIB=${PERL5LIB}:${ENS_CODE_ROOT}/ensembl/modules
$ export PERL5LIB=${PERL5LIB}:${ENS_CODE_ROOT}/ensembl-hive/modules
$ export PERL5LIB=${PERL5LIB}:${ENS_CODE_ROOT}/ensembl-compara/modules # optional but recommended, see 2.7.
$ export PERL5LIB=${PERL5LIB}:${ENSEMBL_CVS_ROOT_DIR}/bioperl-live
$ export PERL5LIB=${PERL5LIB}:${ENSEMBL_CVS_ROOT_DIR}/ensembl/modules
$ export PERL5LIB=${PERL5LIB}:${ENSEMBL_CVS_ROOT_DIR}/ensembl-hive/modules
$ export PERL5LIB=${PERL5LIB}:${ENSEMBL_CVS_ROOT_DIR}/ensembl-compara/modules # optional but recommended, see 2.7.
#
# (for best results, append these lines to your ~/.bashrc configuration file)
# using [t]csh syntax:
$ setenv PERL5LIB ${PERL5LIB}:${ENS_CODE_ROOT}/bioperl-live
$ setenv PERL5LIB ${PERL5LIB}:${ENS_CODE_ROOT}/ensembl/modules
$ setenv PERL5LIB ${PERL5LIB}:${ENS_CODE_ROOT}/ensembl-hive/modules
$ setenv PERL5LIB ${PERL5LIB}:${ENS_CODE_ROOT}/ensembl-compara/modules # optional but recommended, see 2.7.
$ setenv PERL5LIB ${PERL5LIB}:${ENSEMBL_CVS_ROOT_DIR}/bioperl-live
$ setenv PERL5LIB ${PERL5LIB}:${ENSEMBL_CVS_ROOT_DIR}/ensembl/modules
$ setenv PERL5LIB ${PERL5LIB}:${ENSEMBL_CVS_ROOT_DIR}/ensembl-hive/modules
$ setenv PERL5LIB ${PERL5LIB}:${ENSEMBL_CVS_ROOT_DIR}/ensembl-compara/modules # optional but recommended, see 2.7.
#
# (for best results, append these lines to your ~/.cshrc or ~/.tcshrc configuration file)
......
......@@ -46,7 +46,7 @@
You will probably need to specify the following:
$ init_pipeline.pl Bio::EnsEMBL::Hive::PipeConfig::LongMult_conf \
-ensembl_cvs_root_dir $ENS_CODE_ROOT \
-ensembl_cvs_root_dir $ENSEMBL_CVS_ROOT_DIR \
-pipeline_db -host=<your_mysql_host> \
-pipeline_db -user=<your_mysql_username> \
-pipeline_db -user=<your_mysql_password> \
......
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