Talk:Install a local mirror

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Tabix test fails

Testing the custom tabix binary seems to fail. Here's the result:

$ ./tabix -f https://dl.dropboxusercontent.com/u/6959481/bed_hg19.gz chr7:27053199-27373567
[get_local_version] downloading the index file...   
$

If I download the gzip file and run tabix locally, it says the index needs rebuilding:

$ wget https://dl.dropboxusercontent.com/u/6959481/bed_hg19.gz
...
$ ./tabix bed_hg19.gz chr7:27053199-27373567
[tabix] the index file either does not exist or is older than the vcf file. Please reindex.

If I force rebuilding the index on the local file, I get coordinates:

$ ./tabix -f bed_hg19.gz chr7:27053199-27373567
chr7    27132613        27135625        NM_153620       21009   -                       
chr7    27132613        27135625        NM_005522       253     -
...

[ Xin ] The dropbox URLs are no longer working, need to find other HTTPS examples instead.

AlexReynolds (talk) 15:50, 14 March 2014 (PDT)

Archive for installing local browser seems to be inconsistent

It looks like the latest archive for the browser source code is missing some files and has some newer and older files:

$ wget http://epigenomegateway.wustl.edu/info/source/wubrowse.v33.tgz
$ tar zxvf wubrowse.v33.tgz
...

Particularly, the images folder is missing, and other files like base.js have different timestamps and content from the file sukn.tgz.

AlexReynolds (talk) 16:02, 14 March 2014 (PDT)


bwquery test appears to fail

Perhaps bwquery is missing an argument?

# su www-data
\u@\h:\w$ ./bwquery https://dl.dropboxusercontent.com/u/6959481/GSM469970.bigWig chr7 27053199 27373567 20 /tmp/udcCache/x
bwquery: wrong arg
\u@\h:\w$ more /tmp/udcCache/x
/tmp/udcCache/x: No such file or directory

AlexReynolds (talk) 16:23, 14 March 2014 (PDT)


Possible typo in /usr/lib/trash?

Should:

sudo chown www-data.www-data /url/lib/trash

be:

sudo chown www-data:www-data /usr/lib/trash

instead?

AlexReynolds (talk) 16:26, 14 March 2014 (PDT)

Possible type in Compile "bamliquidator" section?

Should:

cd ~/subtleKnife/script/bamliquidator

be:

cd ../subtleKnife/script/bamliquidator

instead?

AlexReynolds (talk) 15:08, 17 March 2014 (PDT)