cobilab / geco3 Goto Github PK

Solving environment: failed

PackagesNotFoundError: The following packages are not available from current channels:

  - geco3

Current channels:

  - https://conda.anaconda.org/bioconda/win-64
  - https://conda.anaconda.org/bioconda/noarch
  - https://repo.anaconda.com/pkgs/main/win-64
  - https://repo.anaconda.com/pkgs/main/noarch
  - https://repo.anaconda.com/pkgs/free/win-64
  - https://repo.anaconda.com/pkgs/free/noarch
  - https://repo.anaconda.com/pkgs/r/win-64
  - https://repo.anaconda.com/pkgs/r/noarch
  - https://repo.anaconda.com/pkgs/pro/win-64
  - https://repo.anaconda.com/pkgs/pro/noarch
  - https://repo.anaconda.com/pkgs/msys2/win-64
  - https://repo.anaconda.com/pkgs/msys2/noarch

To search for alternate channels that may provide the conda package you're
looking for, navigate to  https://anaconda.org and use the search bar at the top of the page 

cd /tmp
mkdir GeCo3-repro-1
cd GeCo3-repro-1
git clone https://github.com/cobilab/geco3.git
cd geco3/src
make
cd ../..
wget http://kirill.med.u-tokai.ac.jp/data/temp/GeCo3-repro-1-test-data.seq.gz
gzip -dc GeCo3-repro-1-test-data.seq.gz >GeCo3-repro-1-test-data.seq
geco3/src/GeCo3 -l 1 GeCo3-repro-1-test-data.seq
geco3/src/GeDe3 GeCo3-repro-1-test-data.seq.co
cmp GeCo3-repro-1-test-data.seq GeCo3-repro-1-test-data.seq.de

lr: 0.03, hs: 40
xs: 35
Total bytes: 347972 (339.8 KB), 1.924 bpb, 1.924 bps w/ no header, Normalized Dissimilarity Rate: 0.962092
Spent 2.37155 sec.
xs: 35
Spent 2.05411 sec.
GeCo3-repro-1-test-data.seq GeCo3-repro-1-test-data.seq.de differ: byte 31, line 1

print "\nInput is named \"GeCo3-repro-1-test-data.seq\"\n";
for (my $l = 1; $l <= 7; $l++)
{
    system("geco3/src/GeCo3 -l $l GeCo3-repro-1-test-data.seq >/dev/null 2>&1");
    system('geco3/src/GeDe3 GeCo3-repro-1-test-data.seq.co >/dev/null 2>&1');
    my $r = `cmp GeCo3-repro-1-test-data.seq GeCo3-repro-1-test-data.seq.de`;
    print "$l: ", (($r eq '') ? "OK\n" : $r);
    unlink 'GeCo3-repro-1-test-data.seq.co';
    unlink 'GeCo3-repro-1-test-data.seq.de';
}
rename 'GeCo3-repro-1-test-data.seq', '1.seq';
print "\nNow input is renamed to \"1.seq\"\n";
for (my $l = 1; $l <= 7; $l++)
{
    system("geco3/src/GeCo3 -l $l 1.seq >/dev/null 2>&1");
    system('geco3/src/GeDe3 1.seq.co >/dev/null 2>&1');
    my $r = `cmp 1.seq 1.seq.de`;
    print "$l: ", (($r eq '') ? "OK\n" : $r);
    unlink '1.seq.co';
    unlink '1.seq.de';
}

cd /tmp
mkdir GeCo3-repro-1-part-2
cd GeCo3-repro-1-part-2
git clone https://github.com/cobilab/geco3.git
cd geco3/src
make
cd ../..
wget http://kirill.med.u-tokai.ac.jp/data/temp/GeCo3-repro-1-test-data.seq.gz
gzip -dc GeCo3-repro-1-test-data.seq.gz >GeCo3-repro-1-test-data.seq
wget http://kirill.med.u-tokai.ac.jp/data/temp/GeCo3-repro-1-test.pl
/usr/bin/env perl GeCo3-repro-1-test.pl

Input is named "GeCo3-repro-1-test-data.seq"
1: GeCo3-repro-1-test-data.seq GeCo3-repro-1-test-data.seq.de differ: byte 31, line 1
2: OK
3: OK
4: GeCo3-repro-1-test-data.seq GeCo3-repro-1-test-data.seq.de differ: byte 40, line 1
5: GeCo3-repro-1-test-data.seq GeCo3-repro-1-test-data.seq.de differ: byte 40, line 1
6: GeCo3-repro-1-test-data.seq GeCo3-repro-1-test-data.seq.de differ: byte 40, line 1
7: OK

Now input is renamed to "1.seq"
1: OK
2: 1.seq 1.seq.de differ: byte 29, line 1
3: 1.seq 1.seq.de differ: byte 17, line 1
4: OK
5: OK
6: OK
7: 1.seq 1.seq.de differ: byte 59, line 1