One common exception is that after you downloaded the Eclipse+Plugin zip file, and while executing the eclipse.exe, this message is shown: “A Java Runtime Environment (JRE) or Java Development Kit (JDK) must be available in order to run Eclipse. No Java virtual machine was found …… javaw.exe in your current path”. This could be due to issues in the Java virtual machine and for almost any cause the solution that we suggest is to reinstall the JRE (Java Runtime Environment) (http://www.oracle.com/technetwork/es/java/javase/downloads/jre7-downloads-1880261.html). Here, you need to choose the Windows x64 (.exe) option (please keep in mind that we only offer Eclipse+Plugin for 64 bit operating systems).
I downloaded the eclipse neon NGSEP plugin and added the shortcut to javaw.exe (64 bit) but having no experience with Eclipse when I get into the Eclipse IDE for Java Developers I have no idea how to run the NGSEP plugin.
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Many thanks for your interest in NGSEP and my apologies for the inconviniences. We are currently working on a completely new graphical interface independent from Eclipse. We hope to release this with a new major version by early next year. By now let us know if you have any further issues running the software.
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Well I had spent a week generating sam files and sorting them to find out that I can't use sam files, they have to be bam files I was misled by this graphic.
Many thanks for your interest in NGSEP and my apologies for the inconviniences. We are currently working on a completely new graphical interface independent from Eclipse. We hope to release this with a new major version by early next year. By now let us know if you have any further issues running the software.
Thanks for your response and my apologies again for the delayed answer. The software usually worked with both SAM and BAM files but we are currently experiencing some issues to process SAM files. We hope to have this bug fixed by the next release. In the mean time, if you use our plugin for mapping, it directly produces sorted BAM files. If you align your reads through the command line, you can either use samtools or picard for sorting and conversion to BAM. In general it is better to work with BAM files because they take up one quarter of the space and hold the same information. You can use samtools in command line or IGV to visualize the information of BAM files
Hope this helps
Jorge
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
One common exception is that after you downloaded the Eclipse+Plugin zip file, and while executing the eclipse.exe, this message is shown: “A Java Runtime Environment (JRE) or Java Development Kit (JDK) must be available in order to run Eclipse. No Java virtual machine was found …… javaw.exe in your current path”. This could be due to issues in the Java virtual machine and for almost any cause the solution that we suggest is to reinstall the JRE (Java Runtime Environment) (http://www.oracle.com/technetwork/es/java/javase/downloads/jre7-downloads-1880261.html). Here, you need to choose the Windows x64 (.exe) option (please keep in mind that we only offer Eclipse+Plugin for 64 bit operating systems).
If you are using a 32 bit operating system you must download first the standard Eclipse (http://www.eclipse.org/downloads/ ) for 32 bit and then download just the plugin (https://sourceforge.net/projects/ngsep/files/OnlyPlugin/ ) and paste it in the dropins folder of your eclipse directory.
If you are experiencing the same problem in MAC please download from the web site (http://www.oracle.com/technetwork/es/java/javase/downloads/jre7-downloads-1880261.html). the Mac OS X x64 Option.
I downloaded the eclipse neon NGSEP plugin and added the shortcut to javaw.exe (64 bit) but having no experience with Eclipse when I get into the Eclipse IDE for Java Developers I have no idea how to run the NGSEP plugin.
Finally found the instructions in Manual for the plugin NGSEP.pdf, they should make this more obvious.
Hi Douglas
Many thanks for your interest in NGSEP and my apologies for the inconviniences. We are currently working on a completely new graphical interface independent from Eclipse. We hope to release this with a new major version by early next year. By now let us know if you have any further issues running the software.
Well I had spent a week generating sam files and sorting them to find out that I can't use sam files, they have to be bam files I was misled by this graphic.
[cid:image001.png@01D5AC1C.31B820B0]
From: Jorge Duitama jduitama@users.sourceforge.net
Sent: Friday, December 6, 2019 9:59 AM
To: [ngsep:discussion] faq@discussion.ngsep.p.re.sourceforge.net
Subject: [ngsep:discussion] No Java virtual machine was found using Eclipse+Plugin option (Windows).
Hi Douglas
Many thanks for your interest in NGSEP and my apologies for the inconviniences. We are currently working on a completely new graphical interface independent from Eclipse. We hope to release this with a new major version by early next year. By now let us know if you have any further issues running the software.
No Java virtual machine was found using Eclipse+Plugin option (Windows).https://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge.net_p_ngsep_discussion_faq_thread_88ba8b69_-3Flimit-3D25-237857&d=DwMCAg&c=7ypwAowFJ8v-mw8AB-SdSueVQgSDL4HiiSaLK01W8HA&r=u5psgUb-1_IPxoNHBeTMVw&m=1zpDXrIoiI8UwCBmtCcADd8ys3JolLAvhZX9VM3qgrA&s=LGoZvjumZa_6SNAMNkrrGH-oReauzgOm4A12Hc_thL8&e=
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Hi Douglas
Thanks for your response and my apologies again for the delayed answer. The software usually worked with both SAM and BAM files but we are currently experiencing some issues to process SAM files. We hope to have this bug fixed by the next release. In the mean time, if you use our plugin for mapping, it directly produces sorted BAM files. If you align your reads through the command line, you can either use samtools or picard for sorting and conversion to BAM. In general it is better to work with BAM files because they take up one quarter of the space and hold the same information. You can use samtools in command line or IGV to visualize the information of BAM files
Hope this helps
Jorge