Where do I find CreateSequenceDictionary.jar? about picard HOT 4 CLOSED

Hi -

There's not a separate CreateSequenceDictionary.jar although it exists in
the picard fat jar. To run it from the command line, run "java -jar
/path/to/picard.jar CreateSequenceDictionary".

On the latter point, I don't think it's asking too much to assume that
someone using a library is at least somewhat familiar with the language the
library is for. If there are specific bits of doc which you think would be
helpful either ask here or if you already know the answer submit a pull
request w/ the extra doc.

J

On Mon, Jan 19, 2015 at 1:03 PM, ginarific [email protected] wrote:

Hi,

I've installed picard and have picard.jar in my dist/ directory. However,
I'm trying to find CreateSequenceDictionary.jar and cannot locate it.

I can find CreateSequenceDictionary.java in src/java/picard/sam but this
not the .jar file. Am I supposed to manually compress it myself? Or are
there additional installation procedures for creating the .jar file?

Finally, I'd like to express my frustration for how ridiculously little
information I've been able to find in the documentation. I'm really
unfamiliar with Java, and I'm not sure why it's assumed that we'd be
familiar with it when working with Picard.

Thanks.

—
Reply to this email directly or view it on GitHub
#152.

from picard.

Ginarific: For future reference, the doc page that answers your usage
question is here:

http://broadinstitute.github.io/picard/command-line-overview.html#Overview

With that, you can run any Picard command, and there is no need for you to
know anything about the Java language.

Best,
Geraldine

On Mon, Jan 19, 2015 at 2:46 PM, Jeff Gentry [email protected]
wrote:

Hi -

There's not a separate CreateSequenceDictionary.jar although it exists in
the picard fat jar. To run it from the command line, run "java -jar
/path/to/picard.jar CreateSequenceDictionary".

On the latter point, I don't think it's asking too much to assume that
someone using a library is at least somewhat familiar with the language
the
library is for. If there are specific bits of doc which you think would be
helpful either ask here or if you already know the answer submit a pull
request w/ the extra doc.

J

On Mon, Jan 19, 2015 at 1:03 PM, ginarific [email protected]
wrote:

Hi,

I've installed picard and have picard.jar in my dist/ directory.
However,
I'm trying to find CreateSequenceDictionary.jar and cannot locate it.

I can find CreateSequenceDictionary.java in src/java/picard/sam but this
not the .jar file. Am I supposed to manually compress it myself? Or are
there additional installation procedures for creating the .jar file?

Finally, I'd like to express my frustration for how ridiculously little
information I've been able to find in the documentation. I'm really
unfamiliar with Java, and I'm not sure why it's assumed that we'd be
familiar with it when working with Picard.

Thanks.

—
Reply to this email directly or view it on GitHub
#152.

—
Reply to this email directly or view it on GitHub
#152 (comment)
.

Geraldine A. Van der Auwera, Ph.D.
Bioinformatics Scientist II
GATK Support & Outreach
Broad Institute

from picard.

Was having the same problem and found that if you download the latest Picard version on sourceforge, it actually contains CreateSequenceDictionary.jar

from picard.

Sourceforge contains previous releases. The latest releases can be found
on github: http://broadinstitute.github.io/picard/

N

On Tue, Feb 10, 2015 at 12:12 PM, Maria Chavez [email protected]
wrote:

Was having the same problem and found that if you download the latest
Picard version from sourceforge, it actually contains
CreateSequenceDictionary.jar

—
Reply to this email directly or view it on GitHub
#152 (comment)
.

from picard.