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scripts_requiring_all.fna.tar.gz [2016/11/17 16:28]
hyjeong created
scripts_requiring_all.fna.tar.gz [2016/11/17 16:29] (current)
hyjeong
Line 1: Line 1:
-$ grep -r "genomes/Bacteria"+====== Scripts requiring old all.fna.tar.gz ======
-Test/test_ima.ini:asmcontigs: ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Candidatus_Carsonella_ruddii_uid58773/NC_008512.fna +
-grep: Utilities/DB/kraken/taxonomy/readme.txt: 허가 거부 +
-Utilities/cpp/Linux-x86_64/kraken/scripts/download_genomic_library.sh:      wget $FTP_SERVER/genomes/Bacteria/all.fna.tar.gz +
-Utilities/cpp/Linux-x86_64/kraken/bin/download_genomic_library.sh:      wget $FTP_SERVER/genomes/Bacteria/all.fna.tar.gz +
-Utilities/cpp/Linux-x86_64/Ray/scripts/NCBI-Taxonomy/CreateRayInputStructures.sh: wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/all.fna.tar.gz +
-Utilities/cpp/Linux-x86_64/Ray/REFIX/NCBI-Taxonomy/CreateRayInputStructures.sh: wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/all.fna.tar.gz +
-Utilities/cpp/Linux-x86_64/ALE/doc/install.rst:   $ wget ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Bacteria/Escherichia_coli_K_12_substr__DH10B_uid20079/CP000948.fna +
-Utilities/cpp/Linux-x86_64/ALE/src/image_maker.py:        wget_command "wget --user anonymous ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Bacteria/Escherichia_coli_K_12_substr__DH10B_uid20079/CP000948.fna" +
-Utilities/cpp/Linux-x86_64/prokka/lib/Phylosift/UpdateDB.pm: my $ncbi_wget_cmd "wget -m --continue --timeout=20 --accept=gbk ftp://ftp.ncbi.nih.gov/genomes/Bacteria"; +
-Utilities/cpp/Linux-x86_64/prokka/lib/Phylosift/UpdateDB.pm: my $FINDER ps_open("find ftp.ncbi.nih.gov/genomes/Bacteria -type d |"); +
-Utilities/cpp/Linux-x86_64/prokka/lib/Phylosift/UpdateDB.pm: my $ncbi_wget_cmd "wget -m --continue --timeout=20 --accept=gbk ftp://ftp.ncbi.nih.gov/genomes/Bacteria_DRAFT"; +
-Utilities/cpp/Linux-x86_64/prokka/lib/Phylosift/UpdateDB.pm: $ncbi_wget_cmd = "wget -m --continue --timeout=20 --accept=\"*fna.tgz\",\"*fna.[0-9].tgz\" ftp://ftp.ncbi.nih.gov/genomes/Bacteria_DRAFT"; +
-Utilities/python/NB_install.py: genomeDir '/genomes/Bacteria' +
-docs/content/workflows.rst:    asmcontigs:         /Users/skoren/Personal/Research/metAMOS/Test/test.asm,ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Candidatus_Carsonella_ruddii_uid58773/NC_008512.fna  +
-phylosift/lib/Phylosift/UpdateDB.pm: my $ncbi_wget_cmd "wget -m --continue --timeout=20 --accept=gbk ftp://ftp.ncbi.nih.gov/genomes/Bacteria"; +
-phylosift/lib/Phylosift/UpdateDB.pm: my $FINDER ps_open("find ftp.ncbi.nih.gov/genomes/Bacteria -type d |"); +
-phylosift/lib/Phylosift/UpdateDB.pm: my $ncbi_wget_cmd = "wget -m --continue --timeout=20 --accept=gbk ftp://ftp.ncbi.nih.gov/genomes/Bacteria_DRAFT"; +
-phylosift/lib/Phylosift/UpdateDB.pm: $ncbi_wget_cmd = "wget -m --continue --timeout=20 --accept=\"*fna.tgz\",\"*fna.[0-9].tgz\" ftp://ftp.ncbi.nih.gov/genomes/Bacteria_DRAFT"; +
-phymm/.logs/setup/01_download_refseq_tarball__err.txt:Can't change remote directory: /genomes/Bacteria: No such file or directory +
-phymm/phymmblSetup.pl:   my $targetDir '/genomes/Bacteria';+
  
 +  $ grep -r "genomes/Bacteria" *
 +  Test/test_ima.ini:asmcontigs: ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Candidatus_Carsonella_ruddii_uid58773/NC_008512.fna
 +  grep: Utilities/DB/kraken/taxonomy/readme.txt: 허가 거부
 +  Utilities/cpp/Linux-x86_64/kraken/scripts/download_genomic_library.sh:      wget $FTP_SERVER/genomes/Bacteria/all.fna.tar.gz
 +  Utilities/cpp/Linux-x86_64/kraken/bin/download_genomic_library.sh:      wget $FTP_SERVER/genomes/Bacteria/all.fna.tar.gz
 +  Utilities/cpp/Linux-x86_64/Ray/scripts/NCBI-Taxonomy/CreateRayInputStructures.sh: wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/all.fna.tar.gz
 +  Utilities/cpp/Linux-x86_64/Ray/REFIX/NCBI-Taxonomy/CreateRayInputStructures.sh: wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/all.fna.tar.gz
 +  Utilities/cpp/Linux-x86_64/ALE/doc/install.rst:   $ wget ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Bacteria/Escherichia_coli_K_12_substr__DH10B_uid20079/CP000948.fna
 +  Utilities/cpp/Linux-x86_64/ALE/src/image_maker.py:        wget_command = "wget --user anonymous ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Bacteria/Escherichia_coli_K_12_substr__DH10B_uid20079/CP000948.fna"
 +  Utilities/cpp/Linux-x86_64/prokka/lib/Phylosift/UpdateDB.pm: my $ncbi_wget_cmd = "wget -m --continue --timeout=20 --accept=gbk ftp://ftp.ncbi.nih.gov/genomes/Bacteria";
 +  Utilities/cpp/Linux-x86_64/prokka/lib/Phylosift/UpdateDB.pm: my $FINDER = ps_open("find ftp.ncbi.nih.gov/genomes/Bacteria -type d |");
 +  Utilities/cpp/Linux-x86_64/prokka/lib/Phylosift/UpdateDB.pm: my $ncbi_wget_cmd = "wget -m --continue --timeout=20 --accept=gbk ftp://ftp.ncbi.nih.gov/genomes/Bacteria_DRAFT";
 +  Utilities/cpp/Linux-x86_64/prokka/lib/Phylosift/UpdateDB.pm: $ncbi_wget_cmd = "wget -m --continue --timeout=20 --accept=\"*fna.tgz\",\"*fna.[0-9].tgz\" ftp://ftp.ncbi.nih.gov/genomes/Bacteria_DRAFT";
 +  Utilities/python/NB_install.py: genomeDir = '/genomes/Bacteria'
 +  docs/content/workflows.rst:    asmcontigs:         /Users/skoren/Personal/Research/metAMOS/Test/test.asm,ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Candidatus_Carsonella_ruddii_uid58773/NC_008512.fna 
 +  phylosift/lib/Phylosift/UpdateDB.pm: my $ncbi_wget_cmd = "wget -m --continue --timeout=20 --accept=gbk ftp://ftp.ncbi.nih.gov/genomes/Bacteria";
 +  phylosift/lib/Phylosift/UpdateDB.pm: my $FINDER = ps_open("find ftp.ncbi.nih.gov/genomes/Bacteria -type d |");
 +  phylosift/lib/Phylosift/UpdateDB.pm: my $ncbi_wget_cmd = "wget -m --continue --timeout=20 --accept=gbk ftp://ftp.ncbi.nih.gov/genomes/Bacteria_DRAFT";
 +  phylosift/lib/Phylosift/UpdateDB.pm: $ncbi_wget_cmd = "wget -m --continue --timeout=20 --accept=\"*fna.tgz\",\"*fna.[0-9].tgz\" ftp://ftp.ncbi.nih.gov/genomes/Bacteria_DRAFT";
 +  phymm/.logs/setup/01_download_refseq_tarball__err.txt:Can't change remote directory: /genomes/Bacteria: No such file or directory
 +  phymm/phymmblSetup.pl:   my $targetDir = '/genomes/Bacteria';
scripts_requiring_all.fna.tar.gz.txt · Last modified: 2016/11/17 16:29 by hyjeong