I am configuring Blast+ on my mac (os sierra) and am having trouble configuring my nr and nt databases that I also downloaded locally. I am trying to follow NCBI's instructions here, and am getting hung up on the Configuration and Example Execution steps.
They say to change my .bash_profile so that it says:
export PATH=$PATH:$HOME/Documents/Luke/Research/Pedulla\ 17-18/blast/ncbi-blast-2.6.0+/bin
That works fine, and they say configure a path for BLASTDB "similarly" but to the file where my DB will be, so I have done this:
export BLASTDB=$BLASTDB:$HOME/Documents/Luke/Research/Pedulla\ 17-18/blast/blastdb/nt.00
which specifies the exact folder that I got when I unzipped the nt tar file from their FTP. With this path, if I run the command...
blastn -query test_query.fa -db nt.00 -task blastn -outfmt "7 qseqid sseqid evalue bitscore" -max_target_seqs 5
then it runs successfully and I get results, but I am worried that these are only being checked against the nt.00 section of the entire nt.00 database file, especially because if I run my test_query.fa sequence on the Web Blast, I get different results.
Also, their instructions say that the path only needs to point to the folder that contains the whole database folder nt.00, from the tar I unzipped--and not the specific nt.00 itself--, which in my case would just be "blastdb/" (As opposed to "blastdb/nt.00/" which then contains nt.00.nhd, nt.00.nal, etc.). That makes sense because when I am working I want to be able to blastn on the nt database but also blastp on the nr one, etc. by changing the -db flag on my command, and there shouldn't be a problem with having them all in this folder, right? But if I must specify the path for BLASTDB with the nt.00 DB added to the end, how could I ever use nr.00 in the same folder (blastdb/)? Essentially, I want to do as the instructions say, and just have this:
export BLASTDB=$BLASTDB:$HOME/Documents/Luke/Research/Pedulla\ 17-18/blast/blastdb/
And then depending on what database I want to use I could just say so after the -db flag on my command. But when I make the path like that above, it gives me this error:
BLAST Database error: No alias or index file found for nucleotide database [nt] in search path [/Users/LJStout::/Users/LJStout/Documents/Luke/Research/Pedulla 17-18/blast/blastdb:]
I have tried running that same blastn command from above and swapping out "nt" for "nt.00", and have tried these commands with the path for BLASTDB ending in both "blastdb/" and "blastdb/nt" and of course "blastdb/nt.00" which is the only one that runs without errors.
Here's an example of another thread I read where the OP is worried about his executions not checking the entire nt.00 folder, this was different than my problem however.
Thanks for you help!
This whole problem came down to having the nt.00 & nr.00 files, the original folders that result from unzipping their respective .tar.gz's, in the same parent folder when it should be that their contents are in the same parent folder. I simply deleted the folders they came in and copied the contents over to my new, singular parent. I was kind of mislead by the instructions, it was a simple mistake. Now, I have one folder, blastdb/ that contains all of the contents of every database I plan on using, including nt,nr, and refseq.
Related
I recently upgraded sqldeveloper to 22.x, I can't remember the previous version it was on. Now commands such as mkdir and spool are failing on scripts I used to run daily.
For example
host mkdir "C:\Users\Isaac\Requests\"
This script was completely unchanged and now it fails with
The filename, directory name, or volume label syntax is incorrect
Spool also fails with
SP2-0556: Invalid file name.
Again, this was a script I would run every single day, for the past year. I can't find what is causing this. Any ideas would be really helpful.
Remove the "quotes"
clear screen
host mkdir c:\Users\JDSMITH\Requests\
cd c:\Users\JDSMITH\Requests\
spool regions.csv
select /*csv*/ * from regions;
spool off
!type regions.csv
!dir
There's a chance this is a side effect of going to Java 11 from Java 8.
If you need a directory name with spaces, you can also use SQLcl.
See the 'sql.exe' in your bin directory, or download latest from oracle.com/sqlcl
Disclaimer: I'm an Oracle employee and a product manager for SQL Developer.
Many PDFs from different courses appear to have been corrupted or something. We first noticed when viewing to view in CHrome and got the error "Failed to load PDF document." In Internet Explorer the page just shows up empty.
When viewing the file in the "Updating file in" area, it says the following: "Either the file does not exist or there is a permission problem." It has a file size, but when I click on Download, the file is 0 kb.
Where are the files saved? Why are they corrupted?
Update: I've narrowed it down to that the /moodledate/filedir lost all the references. The folders are there as well as the files. Is there any way to fix this without having to reupload all PDFs?
I am on version 3.6.3 on Windows
The content/path hash is stored in the mdl_files table - maybe have a look in there to see if you can match up the files. The hash should match the folder/file name.
SELECT *
FROM mdl_files
WHERE filename LIKE '%pdf%'
OR mimetype LIKE '%pdf%'
OR source LIKE '%pdf%'
Also, check the file permissions. I don't use Windows, so not sure how it works on there. But on Linux, the web server should have access to the data folder.
Something like:
sudo chown -R www-data:www-data /pathto/moodledata/
sudo chmod -R 02777 /pathto/moodledata/
see https://docs.moodle.org/38/en/Security_recommendations#Most_secure.2Fparanoid_file_permissions
My team faces the need to encrypt all files in a repository with AES256. For this purpose, we decided we are going to zip all files with such encryption, using the same key for all of them.
The problem we have is that these files sit in a NAS, so from windows boxes they are accessible by \ to them.
The directory structure is something like this:
Original Structure:
Root
-1
|--folder1
|---file1.ext
|---file2.ext
|--folder2
|---filea.ext
|---fileb.ext
|--folder2.a
|---filec.ext
and so on...
Essentially, what we need is to have all the original files contained in a zip file, keeping their original names, which would be something like this:
Desired Outcome:
|-Root
|-1
|--folder1
|---file1.zip
|---file2.zip
|--folder2
|---filea.zip
|---fileb.zip
|--folder2a
|---filec.zip
and so on...
To accomplish this, we tried a batch script that calls 7zip, but it only works if it's run from the root directory, which is something we cannot use as the files are not in a server.
Here is the syntax of the batch script we came up with:
FOR /R %%i IN ("*.wmv") DO "C:\Program Files\7-Zip\7z.exe" a -mx0 -tzip -pPasswordHere "%%~dpni.zip" "%%i"
But, as wrote previously, it only works when run from the root folder, which is something we cannot do as files sit on a network location.
Mapping the drive or making a symbolic link to it doesn't do the trick either.
I've also checked on 7zip to do this, namely, making use of its "-r" operator, but I couldn't find a way to get the desired outcome (namely, recurse through all folders in the remote tree structure -there are a lot of them...- and keep the original file name).
I'm open to any suggestions as any kind of script, trick or guizmo that gets the job done will be more than welcome. =)
Thanks a million in advance!,
Sebas.
----SOLUTION----
I actually found a sollution here, mapping the drive in a different way (it's so simple it just made me feel stupid(er), but it's altogheter beautiful).
Using the batch script below, the remote share can be mapped like so:
You can map a drive using
net use X: \\server\directory
and then you can change to that directory using
pushd X:
(Post from which the answer was taken from: Batch File Iterating through files on a local network server)
I'm using Sphinx on a Linux production server as well as a Windows dev machine running WampServer.
The index configurations in sphinx.conf each require a path setting for the output file name. Because the filesystems on the production server and dev machine are different, I have to have two lines and then comment one out depending on which server I'm using.
#path = /path/to/folder/name #LIVE
path = C:\wamp\www\site\path\to\folder\name #LOCALHOST
Since I have lots of indexes, it gets really old having to constantly comment and uncomment dozens of lines every time I need to update the file.
Using relative paths would be the ideal solution, but when I tried that I received the following error when running the indexer:
FATAL: failed to open ../folder/name.tmp.spl: Invalid argument, will not index. Try --rotate option.
Is it possible to use relative paths in sphinx.conf?
You can use relative paths, but its kind of tricky because you the various utilities will have different working directories.
eg On windows the searchd service, will start IIRC with a working directory of $WINDIR$\System32
on linux, via crontab, I think it has working directory left over from previously, so would have to change the folder in the actual command line
... ie its not relative to the config file, its relative to the current working directory.
Personally I use a version control system (SVN actually) to manage it. The version from Dev, is always the one commited to the repository, the 'working copy' on the LIVE server, has had the paths edited to the right location. So when 'update' to the latest file, only changes are merged leaving the local filepaths in tact.
Other people use a dynamic config file. The config file can be a script (php/python/perl etc) - but this only works on linux so wont help you.
Or can just have a 'publish' script. Basically, you edit a 'master' config file, and one that can be freely copied to all servers. Then a 'publish' script, that writes the apprirate local path. It could do it with some pretty simple search replace.
<?php
if (trim(`hostname`) == 'live') {
$path = '/path/to/folder/';
} else {
$path = 'C:\wamp\www\site\path\to\folder\`;
}
$contents = file_get_contents('sphinx.conf.master');
$contents = str_replace('$path',$path,$contents);
file_put_contents('sphinx.conf',$contents);
Then have path = $path\name in the master config file, which will get replaced to the proper path, when run the script on the local machine
On all my Windows servers, except for one machine, when I execute the following code to allocate a temporary files folder:
use CGI;
my $tmpfile = new CGITempFile(1);
print "tmpfile='", $tmpfile->as_string(), "'\n";
The variable $tmpfile is assigned the value '.\CGItemp1' and this is what I want. But on one of my servers it's incorrectly set to C:\temp\CGItemp1.
All the servers are running Windows 2003 Standard Edition, IIS6 and ActivePerl 5.8.8.822 (upgrading to later version of Perl not an option). The result is always the same when running a script from the command line or in IIS as a CGI script (where scriptmap .pl = c:\perl\bin\perl.exe "%s" %s).
How I can fix this Perl installation and force it to return '.\CGItemp1' by default?
I've even copied the whole Perl folder from one of the working servers to this machine but no joy.
#Hometoast:
I checked the 'TMP' and 'TEMP' environment variables and also $ENV{TMP} and $ENV{TEMP} and they're identical.
From command line they point to the user profile directory, for example:
C:\DOCUME~1\[USERNAME]\LOCALS~1\Temp\1
When run under IIS as a CGI script they both point to:
c:\windows\temp
In registry key HKEY_USERS/.DEFAULT/Environment, both servers have:
%USERPROFILE%\Local Settings\Temp
The ActiveState implementation of CGITempFile() is clearly using an alternative mechanism to determine how it should generate the temporary folder.
#Ranguard:
The real problem is with the CGI.pm module and attachment handling. Whenever a file is uploaded to the site CGI.pm needs to store it somewhere temporary. To do this CGITempFile() is called within CGI.pm to allocate a temporary folder. So unfortunately I can't use File::Temp. Thanks anyway.
#Chris:
That helped a bunch. I did have a quick scan through the CGI.pm source earlier but your suggestion made me go back and look at it more studiously to understand the underlying algorithm. I got things working, but the oddest thing is that there was originally no c:\temp folder on the server.
To obtain a temporary fix I created a c:\temp folder and set the relevant permissions for the website's anonymous user account. But because this is a shared box I couldn't leave things that way, even though the temp files were being deleted. To cut a long story short, I renamed the c:\temp folder to something different and magically the correct '.\' folder path was being returned. I also noticed that the customer had enabled FrontPage extensions on the site, which removes write access for the anonymous user account on the website folders, so this permission needed re-applying. I'm still at a loss as to why at the start of this issue CGITempFile() was returning c:\temp, even though that folder didn't exist, and why it magically started working again.
The name of the temporary directory is held in $CGITempFile::TMPDIRECTORY and initialised in the find_tempdir function in CGI.pm.
The algorithm for choosing the temporary directory is described in the CGI.pm documentation (search for -private_tempfiles).
IIUC, if a C:\Temp folder exists on the server, CGI.pm will use it. If none of the directories checked in find_tempdir exist, then the current directory "." is used.
I hope this helps.
Not the direct answer to your question, but have you tried using File::Temp?
It is specifically designed to work on any OS.
If you're running this script as you, check the %TEMP% environment variable to see if if it differs.
If IIS is executing, check the values in registry for TMP and TEMP under
HKEY_USERS/.DEFAULT/Environment