From 70fe90f1ce47aeb722dd9343c69df66e9d7e1968 Mon Sep 17 00:00:00 2001 From: Mike Lin Date: Sat, 24 Mar 2012 01:08:10 -0400 Subject: [PATCH 1/2] Makefile section for building CDE package --- .gitmodules | 3 +++ CDE | 1 + Makefile | 19 ++++++++++++++++--- cde.options | 54 ++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4 files changed, 74 insertions(+), 3 deletions(-) create mode 160000 CDE create mode 100644 cde.options diff --git a/.gitmodules b/.gitmodules index eb05e36..93325b2 100644 --- a/.gitmodules +++ b/.gitmodules @@ -1,3 +1,6 @@ [submodule "twt"] path = twt url = git://github.com/mlin/twt.git +[submodule "CDE"] + path = CDE + url = git://github.com/pgbovine/CDE.git diff --git a/CDE b/CDE new file mode 160000 index 0000000..36f9f2f --- /dev/null +++ b/CDE @@ -0,0 +1 @@ +Subproject commit 36f9f2f1057545b3b7ec7f8570b6c6dca4c5dcd2 diff --git a/Makefile b/Makefile index a45ca78..b57daba 100644 --- a/Makefile +++ b/Makefile @@ -1,9 +1,10 @@ all: PhyloCSF -.PHONY: PhyloCSF CamlPaml clean +.PHONY: PhyloCSF CamlPaml cde-package CDE clean -ARCH := `uname`.`uname -m` -export ARCH +ARCH := $(shell uname).$(shell uname -m) +PHYLOCSF_BASE := $(shell pwd) +export PHYLOCSF_BASE PhyloCSF: CamlPaml cd src; $(MAKE) clean; $(MAKE) $(MFLAGS) @@ -12,7 +13,19 @@ PhyloCSF: CamlPaml CamlPaml: cd lib/CamlPaml; $(MAKE) $(MFLAGS) reinstall +cde-package: PhyloCSF CDE + CDE/cde ./PhyloCSF.$(ARCH) 12flies PhyloCSF_Examples/tal-AA.fa + CDE/cde ./PhyloCSF.$(ARCH) 29mammals PhyloCSF_Examples/ALDH2.exon5.fa --frames=3 + #CDE/cde ./PhyloCSF.$(ARCH) 29mammals PhyloCSF_Examples/Aldh2.mRNA.fa --frames=3 --removeRefGaps --aa + mv cde-package cde-package.$(ARCH) + tar -cf cde-package.$(ARCH).tar cde-package.$(ARCH) + +CDE: + cd CDE && make + clean: cd lib/CamlPaml; $(MAKE) clean cd src; $(MAKE) clean rm -f PhyloCSF.* + rm -rf cde-package* + cd CDE && make clean || true \ No newline at end of file diff --git a/cde.options b/cde.options new file mode 100644 index 0000000..4826b09 --- /dev/null +++ b/cde.options @@ -0,0 +1,54 @@ +# cde.options v1 (do not alter this first line!) + +# These directories often contain pseudo-files that shouldn't be tracked +ignore_prefix=/dev/ +ignore_exact=/dev +ignore_prefix=/proc/ +ignore_exact=/proc +ignore_prefix=/sys/ +ignore_exact=/sys +ignore_prefix=/var/cache/ +ignore_prefix=/var/lock/ +ignore_prefix=/var/log/ +ignore_prefix=/var/run/ +ignore_prefix=/var/tmp/ +ignore_prefix=/tmp/ +ignore_exact=/tmp + +# un-comment the entries below if you think they might help your app: +#ignore_exact=/etc/ld.so.cache +#ignore_exact=/etc/ld.so.preload +#ignore_exact=/etc/ld.so.nohwcap + +# Ignore .Xauthority to allow X Windows programs to work +ignore_substr=.Xauthority + +# Ignore so that networking can work properly +ignore_exact=/etc/resolv.conf +# These files might be useful to ignore along with /etc/resolv.conf +# (un-comment if you want to try them) +#ignore_exact=/etc/host.conf +#ignore_exact=/etc/hosts +#ignore_exact=/etc/nsswitch.conf +#ignore_exact=/etc/gai.conf + +# Access the target machine's password files: +# (some programs like texmacs need these lines to be commented-out, +# since they try to use home directory paths within the passwd file, +# and those paths might not exist within the package.) +ignore_prefix=/etc/passwd +ignore_prefix=/etc/shadow + +# These environment vars might lead to 'overfitting' and hinder portability +ignore_environment_var=DBUS_SESSION_BUS_ADDRESS +ignore_environment_var=ORBIT_SOCKETDIR +ignore_environment_var=SESSION_MANAGER +ignore_environment_var=XAUTHORITY +ignore_environment_var=DISPLAY + +# For PhyloCSF: allow the dispatch script in our package to set PHYLOCSF_BASE +# so that the parameters and examples can reside at the top level rather than +# buried deep in cde-package/ +ignore_environment_var=PHYLOCSF_BASE +ignore_prefix=/home/mlin/src/PhyloCSF/PhyloCSF_Examples +ignore_prefix=/home/mlin/src/PhyloCSF/PhyloCSF_Parameters From 1f40ece048b9cd31a2e6c019a802fbefbe54c036 Mon Sep 17 00:00:00 2001 From: Irwin Jungreis Date: Thu, 12 Apr 2012 18:01:50 -0400 Subject: [PATCH 2/2] Added 20flies parameter files. (Matrices are copied from 12flies, and tree is from modENCODE.) --- PhyloCSF_Parameters/20flies.nh | 1 + PhyloCSF_Parameters/20flies_coding.ECM | 72 +++++++++++++++++++++++++++++++ PhyloCSF_Parameters/20flies_noncoding.ECM | 72 +++++++++++++++++++++++++++++++ 3 files changed, 145 insertions(+) create mode 100644 PhyloCSF_Parameters/20flies.nh create mode 100644 PhyloCSF_Parameters/20flies_coding.ECM create mode 100644 PhyloCSF_Parameters/20flies_noncoding.ECM diff --git a/PhyloCSF_Parameters/20flies.nh b/PhyloCSF_Parameters/20flies.nh new file mode 100644 index 0000000..67ecba4 --- /dev/null +++ b/PhyloCSF_Parameters/20flies.nh @@ -0,0 +1 @@ +((dgri:0.183954, dvir:0.093575):0.000000, (dmoj:0.110563, ((((dbip:0.034265, dana:0.042476):0.121927, (dkik:0.097564, ((dfic:0.109823, (((dmel:0.023047, (dsim:0.015485, dsec:0.015184):0.013850):0.016088, (dyak:0.026909, dere:0.029818):0.008929):0.047596, (deug:0.102473, (dbia:0.069103, dtak:0.060723):0.015855):0.005098):0.010453):0.008044, (dele:0.062413, drho:0.051516):0.015405):0.046129):0.018695):0.078585, (dper:0.007065, dpse:0.005900):0.185269):0.068212, dwil:0.259408):0.097093):0.035250); diff --git a/PhyloCSF_Parameters/20flies_coding.ECM b/PhyloCSF_Parameters/20flies_coding.ECM new file mode 100644 index 0000000..13c9a37 --- /dev/null +++ b/PhyloCSF_Parameters/20flies_coding.ECM @@ -0,0 +1,72 @@ +0.856979977161 +21.3799807399 0.243048702626 +1.07282632554 23.2891199352 0.417014024371 +1.70189173492 0.188155975062 0. 0.179377976204 +0.0606628059885 1.25594389172 0.0229550444473 0.00328435713687 18.1364766697 +0. 0. 0.566942262009 0.137821071867 31.7666032929 13.2859098957 +0.363302169127 0.3216200572 0.0779713622622 2.07370722097 27.2607785838 28.7642437906 21.1732174575 +11.2727606341 0.582021939541 0.450519061187 0.520525692578 2.87314674986 0.160184415377 0.0417616105268 0.392943810626 +0.197373806562 3.66356232072 0.129128041228 0.379280117156 0.326199666848 2.74555693992 0.150499848254 0.667770340927 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CAT +CCA CCC CCG CCT CGA CGC CGG CGT CTA CTC CTG CTT GAA GAC GAG GAT GCA GCC GCG GCT +GGA GGC GGG GGT GTA GTC GTG GTT TAA TAC TAG TAT TCA TCC TCG TCT TGA TGC TGG TGT +TTA TTC TTG TTT +