User Tools

Site Tools


scripts_requiring_all.fna.tar.gz

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

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