Mercurial > repos > iuc > macs2
changeset 21:b64dcea4531a draft
Uploaded
| author | bgruening |
|---|---|
| date | Fri, 02 May 2014 16:31:01 -0400 |
| parents | f63ccb331626 |
| children | a63785ec271c |
| files | macs2_macros.xml tool_dependencies.xml |
| diffstat | 2 files changed, 4 insertions(+), 3 deletions(-) [+] |
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--- a/macs2_macros.xml Thu May 01 17:07:46 2014 -0400 +++ b/macs2_macros.xml Fri May 02 16:31:01 2014 -0400 @@ -10,7 +10,10 @@ <xml name="conditional_effective_genome_size"> <conditional name="effective_genome_size_options"> - <param name="effective_genome_size_options_selector" type="select" label="Effective genome size" help="--gsize"> + <param name="effective_genome_size_options_selector" type="select" label="Effective genome size" + help="The effective genome size is the portion of the genome that is mappable. Large fractions of the genome are stretches of NNNN that should be discarded. + Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly. + See Table 2 of http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0030377 or http://www.nature.com/nbt/journal/v27/n1/fig_tab/nbt.1518_T1.html for several effective genome sizes. (--gsize)"> <option value="2451960000">Human (2.451.960.000)</option> <option value="2150570000">Mouse (2.150.570.000)</option> <option value="121400000">Fly (121.400.000)</option>
--- a/tool_dependencies.xml Thu May 01 17:07:46 2014 -0400 +++ b/tool_dependencies.xml Fri May 02 16:31:01 2014 -0400 @@ -38,8 +38,6 @@ <!-- exporting the CFLAGS and CPPFLAGS are due to http://stackoverflow.com/questions/22313407/clang-error-unknown-argument-mno-fused-madd-python-package-installation-fa --> <action type="shell_command"> export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python && - export CFLAGS=-Qunused-arguments && - export CPPFLAGS=-Qunused-arguments && python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin </action> <action type="set_environment">