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Re: [Vcftools-help] on svn update
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From: Mao J. <jia...@gm...> - 2010-12-31 14:30:16
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Dear Mr. Adam, Thanks and Happy new year. Jian-Feng 2010/12/31 Adam Auton <ada...@gm...>: > That part of VCFtools (i.e. the Perl module) isn't my speciality, so I'm > hoping someone else will be able to help you. > A > > On 31 December 2010 14:24, Mao Jianfeng <jia...@gm...> wrote: >> >> Dear Mr. Adam, >> >> Thanks for your kind help. >> >> I have posted a thread in VCFtools list, named "VCF file can not be >> read and merged after it was compressed,Why?". I think that is not a >> difficult problem. But, I am a newbie. I need helps and directions. >> >> Note: tabix has been in my path. But, I can not merge the VCF files in >> the EXAMPLES folder. >> >> Jian-Feng >> >> >> >> >> 2010/12/31 Adam Auton <ada...@gm...>: >> > If the svn checkout worked, then you are at the latest version. >> > A >> > >> > On 31 December 2010 14:08, Mao Jianfeng <jia...@gm...> wrote: >> >> >> >> Dear Adam, >> >> >> >> Following your advice, I firstly ran "svn checkout >> >> https://vcftools.svn.sourceforge.net/svnroot/vcftools vcftools", and >> >> then "svn update". But, I still got "Skipped '.' ". >> >> >> >> Could you please give me any direction? >> >> >> >> I expect your helps. >> >> >> >> Jian-Feng >> >> >> >> >> >> >> >> abt6-mao-mbp:tabix-0.2.3 jianfengmao$ svn checkout >> >> https://vcftools.svn.sourceforge.net/svnroot/vcftools vcftools >> >> A vcftools/file_release >> >> A vcftools/file_release/vcftools_0.1.1_source.tar.gz >> >> A vcftools/file_release/VCFtools_0.1.3.1.tar.gz >> >> A vcftools/file_release/vcftools_0.1.2_source.tar.gz >> >> A vcftools/file_release/vcftools_0.1_source.tar.gz >> >> A vcftools/file_release/VCFtools_0.1.3.2.tar.gz >> >> A vcftools/file_release/VCFtools_0.1.3.tar.gz >> >> A vcftools/file_release/vcftools_0.1.1_source_old.tar.gz >> >> A vcftools/cpp >> >> A vcftools/cpp/vcf_entry.cpp >> >> A vcftools/cpp/vcftools.cpp >> >> A vcftools/cpp/output_log.cpp >> >> A vcftools/cpp/parameters.cpp >> >> A vcftools/cpp/vcf_entry.h >> >> A vcftools/cpp/vcftools.h >> >> A vcftools/cpp/vcf_file_diff.cpp >> >> A vcftools/cpp/vcf_file_filters.cpp >> >> A vcftools/cpp/output_log.h >> >> A vcftools/cpp/parameters.h >> >> A vcftools/cpp/vcf_entry_setters.cpp >> >> A vcftools/cpp/vcf_file.cpp >> >> A vcftools/cpp/vcf_file.h >> >> A vcftools/cpp/Makefile >> >> A vcftools/cpp/vcf_entry_getters.cpp >> >> A vcftools/cpp/vcf_file_output.cpp >> >> A vcftools/perl >> >> A vcftools/perl/vcf-subset >> >> A vcftools/perl/FaSlice.pm >> >> A vcftools/perl/query-vcf >> >> A vcftools/perl/test.t >> >> A vcftools/perl/vcf-concat >> >> A vcftools/perl/vcf-annotate >> >> A vcftools/perl/ChangeLog >> >> A vcftools/perl/Vcf.pm >> >> A vcftools/perl/vcf-convert >> >> A vcftools/perl/vcf-isec >> >> A vcftools/perl/vcf-validator >> >> A vcftools/perl/vcf-to-tab >> >> A vcftools/perl/compare-vcf >> >> A vcftools/perl/vcf-sort >> >> A vcftools/perl/fill-an-ac >> >> A vcftools/perl/fill-aa >> >> A vcftools/perl/vcf-shuffle-cols >> >> A vcftools/perl/fill-rsIDs >> >> A vcftools/perl/VcfStats.pm >> >> A vcftools/perl/vcf-stats >> >> A vcftools/perl/merge-vcf >> >> A vcftools/perl/Makefile >> >> A vcftools/website >> >> A vcftools/website/VCF-poster.pdf >> >> A vcftools/website/specs.html >> >> A vcftools/website/src >> >> A vcftools/website/src/index.inc >> >> A vcftools/website/src/perl_module.inc >> >> A vcftools/website/src/docs.inc >> >> A vcftools/website/src/options.inc >> >> A vcftools/website/src/specs.inc >> >> A vcftools/website/src/license.inc >> >> A vcftools/website/src/index.php >> >> A vcftools/website/favicon.png >> >> A vcftools/website/default.css >> >> A vcftools/website/img >> >> A vcftools/website/img/bgcontainer.gif >> >> A vcftools/website/img/quote.gif >> >> A vcftools/website/img/bgcode.gif >> >> A vcftools/website/img/li.gif >> >> A vcftools/website/img/search.gif >> >> A vcftools/website/img/bg.gif >> >> A vcftools/website/img/header.gif >> >> A vcftools/website/img/bgul.gif >> >> A vcftools/website/Makefile >> >> A vcftools/website/README >> >> A vcftools/website/favicon.ico >> >> A vcftools/.project >> >> A vcftools/.cproject >> >> A vcftools/README.txt >> >> A vcftools/Makefile >> >> A vcftools/.settings >> >> A vcftools/.settings/org.eclipse.ltk.core.refactoring.prefs >> >> A vcftools/examples >> >> A vcftools/examples/annotate.out >> >> A vcftools/examples/subset.vcf >> >> A vcftools/examples/shuffle-test.vcf >> >> A vcftools/examples/annotate.txt >> >> A vcftools/examples/cmp-test-a.vcf >> >> A vcftools/examples/subset.indels.out >> >> A vcftools/examples/query-test.out >> >> A vcftools/examples/cmp-test-a-3.3.vcf >> >> A vcftools/examples/cmp-test-b.vcf >> >> A vcftools/examples/cmp-test-b-3.3.vcf >> >> A vcftools/examples/subset.SNPs.out >> >> A vcftools/examples/merge-test.vcf.out >> >> A vcftools/examples/isec-n2-test.vcf.out >> >> A vcftools/examples/annotate2.out >> >> A vcftools/examples/concat-a.vcf >> >> A vcftools/examples/invalid-4.0.vcf >> >> A vcftools/examples/cmp-test.out >> >> A vcftools/examples/concat-b.vcf >> >> A vcftools/examples/annotate-test.vcf >> >> A vcftools/examples/concat-c.vcf >> >> A vcftools/examples/merge-test-a.vcf >> >> A vcftools/examples/merge-test-b.vcf >> >> A vcftools/examples/valid-4.0.vcf.stats >> >> A vcftools/examples/merge-test-c.vcf >> >> A vcftools/examples/valid-4.0.vcf >> >> A vcftools/examples/concat.out >> >> A vcftools/examples/valid-3.3.vcf >> >> U vcftools >> >> Checked out revision 399. >> >> abt6-mao-mbp:tabix-0.2.3 jianfengmao$ svn update >> >> Skipped '.' >> >> >> >> >> >> >> >> >> >> >> >> 2010/12/31 Adam Auton <ada...@gm...>: >> >> > Did you run the following command before using "svn update"? >> >> > svn checkout https://vcftools.svn.sourceforge.net/svnroot/vcftools >> >> > vcftools >> >> > Kind regards, >> >> > Adam >> >> > >> >> > On 31 December 2010 13:28, Mao Jianfeng <jia...@gm...> >> >> > wrote: >> >> >> >> >> >> Dear VCFtools helpers, >> >> >> >> >> >> I am new to Unix and genomics. >> >> >> >> >> >> When I intent to update VCFtools, I got "Skipped ''."". I want to >> >> >> know >> >> >> what it is meaning. >> >> >> >> >> >> Thank you in Advance. >> >> >> >> >> >> Best. >> >> >> >> >> >> abt6-mao-mbp:tabix-0.2.3 jianfengmao$ svn update >> >> >> Skipped '.' >> >> >> >> >> >> >> >> >> -- >> >> >> Jian-Feng, Mao >> >> >> >> >> >> the Institute of Botany, >> >> >> Chinese Academy of Botany, >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> ------------------------------------------------------------------------------ >> >> >> Learn how Oracle Real Application Clusters (RAC) One Node allows >> >> >> customers >> >> >> to consolidate database storage, standardize their database >> >> >> environment, >> >> >> and, >> >> >> should the need arise, upgrade to a full multi-node Oracle RAC >> >> >> database >> >> >> without downtime or disruption >> >> >> http://p.sf.net/sfu/oracle-sfdevnl >> >> >> _______________________________________________ >> >> >> Vcftools-help mailing list >> >> >> Vcf...@li... >> >> >> https://lists.sourceforge.net/lists/listinfo/vcftools-help >> >> > >> >> > >> >> > >> > >> > >> > >> > >> >> >> >> -- >> Jian-Feng, Mao >> >> the Institute of Botany, >> Chinese Academy of Botany, > > > > -- > Adam Auton > Post-Doctoral Research Scientist, > Wellcome Trust Centre for Human Genetics, > University of Oxford > Roosevelt Drive > Oxford > OX3 7BN > UK > -- Jian-Feng, Mao the Institute of Botany, Chinese Academy of Botany, |
