From c6918180597a4516223c692815ba0e5e25074ca8 Mon Sep 17 00:00:00 2001 From: Eric Coissac Date: Thu, 5 Apr 2018 18:03:51 +0200 Subject: [PATCH] Changes in .gitignore Former-commit-id: 7e9fcd4ed6487e52562b274d87345e0e46f1458d Former-commit-id: bf7a58dcf96db9f8c132977aa7d3f6af97cce0f5 --- .gitignore | 5 + data/.gitignore | 2 + data/cds/.gitignore | 1 + data/cds/chlorodb/.gitignore | 1 + data/cds/chlorodb/core/.gitignore | 1 + data/cds/chlorodb/download/.gitignore | 1 + data/nucrrna/plants/.gitignore | 6 + data/rrna/.gitignore | 13 ++ detectors/.gitignore | 1 + detectors/normalize/bin/.gitignore | 1 + detectors/nucrrna/bin/.gitignore | 1 + detectors/rrna/tools/.gitignore | 1 + detectors/trna/tools/.gitignore | 1 + src/.gitignore | 3 + src/ITSx/.gitignore | 1 + src/_unix_tools_/.gitignore | 1 + src/clustalo/.gitignore | 1 + src/exonerate/glib2/.gitignore | 1 + src/exonerate/pkg-config/.gitignore | 1 + src/gawk/.gitignore | 1 + src/getopt/.gitignore | 1 + src/hmmer3/.gitignore | 1 + src/kimono/lxpack/src/.gitignore | 13 ++ src/muscle/.gitignore | 1 + src/muscle/muscle3.8.31/.gitignore | 148 +++++++++++++++++ src/muscle/muscle3.8.31/src/.gitignore | 150 ++++++++++++++++++ src/ncbiblast/binaries/.gitignore | 1 + src/prokov/lxpack/src/.gitignore | 9 ++ src/sumaclust/.gitignore | 1 + .../sumalibs/libfasta/.gitignore | 6 + .../sumalibs/libfile/.gitignore | 2 + .../sumatra-1.0.10/sumalibs/liblcs/.gitignore | 3 + .../sumalibs/libutils/.gitignore | 3 + src/tcsh/.gitignore | 2 + src/trnascan-se/.gitignore | 1 + 35 files changed, 386 insertions(+) create mode 100644 data/.gitignore create mode 100644 data/cds/.gitignore create mode 100644 data/cds/chlorodb/.gitignore create mode 100644 data/cds/chlorodb/download/.gitignore create mode 100644 data/nucrrna/plants/.gitignore create mode 100644 data/rrna/.gitignore create mode 100644 detectors/.gitignore create mode 100644 detectors/normalize/bin/.gitignore create mode 100644 detectors/nucrrna/bin/.gitignore create mode 100644 detectors/rrna/tools/.gitignore create mode 100644 detectors/trna/tools/.gitignore create mode 100644 src/.gitignore create mode 100644 src/ITSx/.gitignore create mode 100644 src/_unix_tools_/.gitignore create mode 100644 src/clustalo/.gitignore create mode 100644 src/kimono/lxpack/src/.gitignore create mode 100644 src/muscle/.gitignore create mode 100644 src/muscle/muscle3.8.31/.gitignore create mode 100644 src/muscle/muscle3.8.31/src/.gitignore create mode 100644 src/prokov/lxpack/src/.gitignore create mode 100644 src/sumaclust/.gitignore create mode 100644 src/sumatra/sumatra-1.0.10/sumalibs/libfasta/.gitignore create mode 100644 src/sumatra/sumatra-1.0.10/sumalibs/libfile/.gitignore create mode 100644 src/sumatra/sumatra-1.0.10/sumalibs/liblcs/.gitignore create mode 100644 src/sumatra/sumatra-1.0.10/sumalibs/libutils/.gitignore create mode 100644 src/tcsh/.gitignore create mode 100644 src/trnascan-se/.gitignore diff --git a/.gitignore b/.gitignore index 1933786..23318ac 100644 --- a/.gitignore +++ b/.gitignore @@ -1 +1,6 @@ /test/ +/.DS_Store +/samples/ +/toto.embl +/toto.fasta +/toto.log diff --git a/data/.gitignore b/data/.gitignore new file mode 100644 index 0000000..0ae624f --- /dev/null +++ b/data/.gitignore @@ -0,0 +1,2 @@ +/its/ +/.DS_Store diff --git a/data/cds/.gitignore b/data/cds/.gitignore new file mode 100644 index 0000000..9bb88d3 --- /dev/null +++ b/data/cds/.gitignore @@ -0,0 +1 @@ +/.DS_Store diff --git a/data/cds/chlorodb/.gitignore b/data/cds/chlorodb/.gitignore new file mode 100644 index 0000000..9bb88d3 --- /dev/null +++ b/data/cds/chlorodb/.gitignore @@ -0,0 +1 @@ +/.DS_Store diff --git a/data/cds/chlorodb/core/.gitignore b/data/cds/chlorodb/core/.gitignore index e831788..0cdf47c 100644 --- a/data/cds/chlorodb/core/.gitignore +++ b/data/cds/chlorodb/core/.gitignore @@ -79,3 +79,4 @@ /ycf2/ /ycf3/ /ycf4/ +/.DS_Store diff --git a/data/cds/chlorodb/download/.gitignore b/data/cds/chlorodb/download/.gitignore new file mode 100644 index 0000000..9bb88d3 --- /dev/null +++ b/data/cds/chlorodb/download/.gitignore @@ -0,0 +1 @@ +/.DS_Store diff --git a/data/nucrrna/plants/.gitignore b/data/nucrrna/plants/.gitignore new file mode 100644 index 0000000..b240b68 --- /dev/null +++ b/data/nucrrna/plants/.gitignore @@ -0,0 +1,6 @@ +/nuc_RRNA_18S_RC.fst +/nuc_RRNA_18S_RC.hmm +/nuc_RRNA_18S.hmm +/nuc_RRNA_28S_RC.fst +/nuc_RRNA_28S_RC.hmm +/nuc_RRNA_28S.hmm diff --git a/data/rrna/.gitignore b/data/rrna/.gitignore new file mode 100644 index 0000000..2cc6589 --- /dev/null +++ b/data/rrna/.gitignore @@ -0,0 +1,13 @@ +/16S.goodali.rc.fst +/23S.goodali.rc.fst +/4.5S.goodali.rc.fst +/5S.goodali.rc.fst +/plast_RRNA_16S_RC.hmm +/plast_RRNA_16S.hmm +/plast_RRNA_23S_RC.hmm +/plast_RRNA_23S.hmm +/plast_RRNA_4.5S_RC.hmm +/plast_RRNA_4.5S.hmm +/plast_RRNA_5S_RC.hmm +/plast_RRNA_5S.hmm +/.DS_Store diff --git a/detectors/.gitignore b/detectors/.gitignore new file mode 100644 index 0000000..9bb88d3 --- /dev/null +++ b/detectors/.gitignore @@ -0,0 +1 @@ +/.DS_Store diff --git a/detectors/normalize/bin/.gitignore b/detectors/normalize/bin/.gitignore new file mode 100644 index 0000000..0ed0658 --- /dev/null +++ b/detectors/normalize/bin/.gitignore @@ -0,0 +1 @@ +/draft diff --git a/detectors/nucrrna/bin/.gitignore b/detectors/nucrrna/bin/.gitignore new file mode 100644 index 0000000..0ed0658 --- /dev/null +++ b/detectors/nucrrna/bin/.gitignore @@ -0,0 +1 @@ +/draft diff --git a/detectors/rrna/tools/.gitignore b/detectors/rrna/tools/.gitignore new file mode 100644 index 0000000..0ed0658 --- /dev/null +++ b/detectors/rrna/tools/.gitignore @@ -0,0 +1 @@ +/draft diff --git a/detectors/trna/tools/.gitignore b/detectors/trna/tools/.gitignore new file mode 100644 index 0000000..0ed0658 --- /dev/null +++ b/detectors/trna/tools/.gitignore @@ -0,0 +1 @@ +/draft diff --git a/src/.gitignore b/src/.gitignore new file mode 100644 index 0000000..a55be8c --- /dev/null +++ b/src/.gitignore @@ -0,0 +1,3 @@ +/.DS_Store +/trnascan-se/ +/gnuplot/ diff --git a/src/ITSx/.gitignore b/src/ITSx/.gitignore new file mode 100644 index 0000000..3f0916a --- /dev/null +++ b/src/ITSx/.gitignore @@ -0,0 +1 @@ +/build.i386-darwin/ diff --git a/src/_unix_tools_/.gitignore b/src/_unix_tools_/.gitignore new file mode 100644 index 0000000..9bb88d3 --- /dev/null +++ b/src/_unix_tools_/.gitignore @@ -0,0 +1 @@ +/.DS_Store diff --git a/src/clustalo/.gitignore b/src/clustalo/.gitignore new file mode 100644 index 0000000..9bb88d3 --- /dev/null +++ b/src/clustalo/.gitignore @@ -0,0 +1 @@ +/.DS_Store diff --git a/src/exonerate/glib2/.gitignore b/src/exonerate/glib2/.gitignore index 3f0916a..1169098 100644 --- a/src/exonerate/glib2/.gitignore +++ b/src/exonerate/glib2/.gitignore @@ -1 +1,2 @@ /build.i386-darwin/ +/.DS_Store diff --git a/src/exonerate/pkg-config/.gitignore b/src/exonerate/pkg-config/.gitignore index 3f0916a..1169098 100644 --- a/src/exonerate/pkg-config/.gitignore +++ b/src/exonerate/pkg-config/.gitignore @@ -1 +1,2 @@ /build.i386-darwin/ +/.DS_Store diff --git a/src/gawk/.gitignore b/src/gawk/.gitignore index 45e8faf..48e5068 100644 --- a/src/gawk/.gitignore +++ b/src/gawk/.gitignore @@ -1,2 +1,3 @@ /build.i386-darwin/ /gawk-4/ +/.DS_Store diff --git a/src/getopt/.gitignore b/src/getopt/.gitignore index 3f0916a..1169098 100644 --- a/src/getopt/.gitignore +++ b/src/getopt/.gitignore @@ -1 +1,2 @@ /build.i386-darwin/ +/.DS_Store diff --git a/src/hmmer3/.gitignore b/src/hmmer3/.gitignore index 3f0916a..1169098 100644 --- a/src/hmmer3/.gitignore +++ b/src/hmmer3/.gitignore @@ -1 +1,2 @@ /build.i386-darwin/ +/.DS_Store diff --git a/src/kimono/lxpack/src/.gitignore b/src/kimono/lxpack/src/.gitignore new file mode 100644 index 0000000..d3ddbbd --- /dev/null +++ b/src/kimono/lxpack/src/.gitignore @@ -0,0 +1,13 @@ +/fasta_io.o +/kim_alphabet.o +/kim_codonskew.o +/kim_counter.o +/kim_distance.o +/kim_genetic.o +/kim_indexer.o +/kim_mixer.o +/kim_sequence.o +/kim_util.o +/kim_zone.o +/kimfit +/kimono diff --git a/src/muscle/.gitignore b/src/muscle/.gitignore new file mode 100644 index 0000000..9bb88d3 --- /dev/null +++ b/src/muscle/.gitignore @@ -0,0 +1 @@ +/.DS_Store diff --git a/src/muscle/muscle3.8.31/.gitignore b/src/muscle/muscle3.8.31/.gitignore new file mode 100644 index 0000000..007633c --- /dev/null +++ b/src/muscle/muscle3.8.31/.gitignore @@ -0,0 +1,148 @@ +/aligngivenpath.o +/aligngivenpathsw.o +/aligntwomsas.o +/aligntwoprofs.o +/aln.o +/alpha.o +/anchors.o +/bittraceback.o +/blosum62.o +/blosumla.o +/clust.o +/cluster.o +/clwwt.o +/color.o +/cons.o +/diaglist.o +/diffobjscore.o +/diffpaths.o +/difftrees.o +/difftreese.o +/distcalc.o +/distfunc.o +/distpwkimura.o +/domuscle.o +/dosp.o +/dpreglist.o +/drawtree.o +/edgelist.o +/enumopts.o +/enumtostr.o +/estring.o +/fasta.o +/fasta2.o +/fastclust.o +/fastdist.o +/fastdistjones.o +/fastdistkbit.o +/fastdistkmer.o +/fastdistmafft.o +/fastdistnuc.o +/fastscorepath2.o +/finddiags.o +/finddiagsn.o +/glbalign.o +/glbalign352.o +/glbaligndiag.o +/glbalignle.o +/glbalignsimple.o +/glbalignsp.o +/glbalignspn.o +/glbalignss.o +/glbalndimer.o +/globals.o +/globalslinux.o +/globalsosx.o +/globalsother.o +/globalswin32.o +/gonnet.o +/henikoffweight.o +/henikoffweightpb.o +/html.o +/hydro.o +/intmath.o +/local.o +/main.o +/makerootmsa.o +/makerootmsab.o +/maketree.o +/mhack.o +/mpam200.o +/msa.o +/msa2.o +/msadistkimura.o +/msf.o +/muscle +/muscle.o +/muscleout.o +/nucmx.o +/nwdasimple.o +/nwdasimple2.o +/nwdasmall.o +/nwrec.o +/nwsmall.o +/objscore.o +/objscore2.o +/objscoreda.o +/onexception.o +/options.o +/outweights.o +/pam200mafft.o +/params.o +/phy.o +/phy2.o +/phy3.o +/phy4.o +/phyfromclust.o +/phyfromfile.o +/physeq.o +/phytofile.o +/posgap.o +/ppscore.o +/profdb.o +/profile.o +/profilefrommsa.o +/progalign.o +/progress.o +/progressivealign.o +/pwpath.o +/readmx.o +/realigndiffs.o +/realigndiffse.o +/refine.o +/refinehoriz.o +/refinesubfams.o +/refinetree.o +/refinetreee.o +/refinevert.o +/refinew.o +/savebest.o +/scoredist.o +/scoregaps.o +/scorehistory.o +/scorepp.o +/seq.o +/seqvect.o +/setblosumweights.o +/setgscweights.o +/setnewhandler.o +/spfast.o +/sptest.o +/stabilize.o +/subfam.o +/subfams.o +/sw.o +/termgaps.o +/textfile.o +/threewaywt.o +/tomhydro.o +/traceback.o +/tracebackopt.o +/tracebacksw.o +/treefrommsa.o +/typetostr.o +/upgma2.o +/usage.o +/validateids.o +/vtml2.o +/writescorefile.o diff --git a/src/muscle/muscle3.8.31/src/.gitignore b/src/muscle/muscle3.8.31/src/.gitignore new file mode 100644 index 0000000..901690d --- /dev/null +++ b/src/muscle/muscle3.8.31/src/.gitignore @@ -0,0 +1,150 @@ +/aligngivenpath.o +/aligngivenpathsw.o +/aligntwomsas.o +/aligntwoprofs.o +/aln.o +/alpha.o +/anchors.o +/bittraceback.o +/blosum62.o +/blosumla.o +/clust.o +/cluster.o +/clwwt.o +/color.o +/cons.o +/diaglist.o +/diffobjscore.o +/diffpaths.o +/difftrees.o +/difftreese.o +/distcalc.o +/distfunc.o +/distpwkimura.o +/domuscle.o +/dosp.o +/dpreglist.o +/drawtree.o +/edgelist.o +/enumopts.o +/enumtostr.o +/estring.o +/fasta.o +/fasta2.o +/fastclust.o +/fastdist.o +/fastdistjones.o +/fastdistkbit.o +/fastdistkmer.o +/fastdistmafft.o +/fastdistnuc.o +/fastscorepath2.o +/finddiags.o +/finddiagsn.o +/glbalign.o +/glbalign352.o +/glbaligndiag.o +/glbalignle.o +/glbalignsimple.o +/glbalignsp.o +/glbalignspn.o +/glbalignss.o +/glbalndimer.o +/globals.o +/globalslinux.o +/globalsosx.o +/globalsother.o +/globalswin32.o +/gonnet.o +/henikoffweight.o +/henikoffweightpb.o +/html.o +/hydro.o +/intmath.o +/local.o +/main.o +/makerootmsa.o +/makerootmsab.o +/maketree.o +/mhack.o +/mpam200.o +/msa.o +/msa2.o +/msadistkimura.o +/msf.o +/muscle +/muscle.make.stderr.txt +/muscle.make.stdout.txt +/muscle.o +/muscleout.o +/nucmx.o +/nwdasimple.o +/nwdasimple2.o +/nwdasmall.o +/nwrec.o +/nwsmall.o +/objscore.o +/objscore2.o +/objscoreda.o +/onexception.o +/options.o +/outweights.o +/pam200mafft.o +/params.o +/phy.o +/phy2.o +/phy3.o +/phy4.o +/phyfromclust.o +/phyfromfile.o +/physeq.o +/phytofile.o +/posgap.o +/ppscore.o +/profdb.o +/profile.o +/profilefrommsa.o +/progalign.o +/progress.o +/progressivealign.o +/pwpath.o +/readmx.o +/realigndiffs.o +/realigndiffse.o +/refine.o +/refinehoriz.o +/refinesubfams.o +/refinetree.o +/refinetreee.o +/refinevert.o +/refinew.o +/savebest.o +/scoredist.o +/scoregaps.o +/scorehistory.o +/scorepp.o +/seq.o +/seqvect.o +/setblosumweights.o +/setgscweights.o +/setnewhandler.o +/spfast.o +/sptest.o +/stabilize.o +/subfam.o +/subfams.o +/sw.o +/termgaps.o +/textfile.o +/threewaywt.o +/tomhydro.o +/traceback.o +/tracebackopt.o +/tracebacksw.o +/treefrommsa.o +/typetostr.o +/upgma2.o +/usage.o +/validateids.o +/vtml2.o +/writescorefile.o diff --git a/src/ncbiblast/binaries/.gitignore b/src/ncbiblast/binaries/.gitignore index 5b0895b..0de5d9c 100644 --- a/src/ncbiblast/binaries/.gitignore +++ b/src/ncbiblast/binaries/.gitignore @@ -1 +1,2 @@ /bin.i386-darwin/ +/.DS_Store diff --git a/src/prokov/lxpack/src/.gitignore b/src/prokov/lxpack/src/.gitignore new file mode 100644 index 0000000..a9e9391 --- /dev/null +++ b/src/prokov/lxpack/src/.gitignore @@ -0,0 +1,9 @@ +/fasta_io.o +/libkov_io.o +/libkov_proba.o +/libkov_util.o +/prokov_cds +/prokov_curve +/prokov_learn +/prokov_orf +/prokov_score diff --git a/src/sumaclust/.gitignore b/src/sumaclust/.gitignore new file mode 100644 index 0000000..9bb88d3 --- /dev/null +++ b/src/sumaclust/.gitignore @@ -0,0 +1 @@ +/.DS_Store diff --git a/src/sumatra/sumatra-1.0.10/sumalibs/libfasta/.gitignore b/src/sumatra/sumatra-1.0.10/sumalibs/libfasta/.gitignore new file mode 100644 index 0000000..141ef27 --- /dev/null +++ b/src/sumatra/sumatra-1.0.10/sumalibs/libfasta/.gitignore @@ -0,0 +1,6 @@ +/fasta_header_handler.o +/fasta_header_parser.o +/fasta_seq_writer.o +/header_mem_handler.o +/libfasta.a +/sequence.o diff --git a/src/sumatra/sumatra-1.0.10/sumalibs/libfile/.gitignore b/src/sumatra/sumatra-1.0.10/sumalibs/libfile/.gitignore new file mode 100644 index 0000000..2d356ae --- /dev/null +++ b/src/sumatra/sumatra-1.0.10/sumalibs/libfile/.gitignore @@ -0,0 +1,2 @@ +/fileHandling.o +/libfile.a diff --git a/src/sumatra/sumatra-1.0.10/sumalibs/liblcs/.gitignore b/src/sumatra/sumatra-1.0.10/sumalibs/liblcs/.gitignore new file mode 100644 index 0000000..cce097b --- /dev/null +++ b/src/sumatra/sumatra-1.0.10/sumalibs/liblcs/.gitignore @@ -0,0 +1,3 @@ +/liblcs.a +/sse_banded_LCS_alignment.o +/upperband.o diff --git a/src/sumatra/sumatra-1.0.10/sumalibs/libutils/.gitignore b/src/sumatra/sumatra-1.0.10/sumalibs/libutils/.gitignore new file mode 100644 index 0000000..6a80a09 --- /dev/null +++ b/src/sumatra/sumatra-1.0.10/sumalibs/libutils/.gitignore @@ -0,0 +1,3 @@ +/debug.o +/libutils.a +/utilities.o diff --git a/src/tcsh/.gitignore b/src/tcsh/.gitignore new file mode 100644 index 0000000..1169098 --- /dev/null +++ b/src/tcsh/.gitignore @@ -0,0 +1,2 @@ +/build.i386-darwin/ +/.DS_Store diff --git a/src/trnascan-se/.gitignore b/src/trnascan-se/.gitignore new file mode 100644 index 0000000..9bb88d3 --- /dev/null +++ b/src/trnascan-se/.gitignore @@ -0,0 +1 @@ +/.DS_Store