Re: Help needed to update to latest fastqc
Hi Olivier, On Wed, Nov 04, 2015 at 01:50:36PM +0100, Olivier Sallou wrote: > sorry, I forgot to upload libsis-hdf5-java after libsis-base-java being > accepted in sid. > libsis-hdf5-java has just been uploaded (the one you need I think), we > need to wait to get it accepted in sid. Cool. I just added the Build-Depends to fastqc in Git to have a record about this. Thanks for your great work Andreas. -- http://fam-tille.de
Re: Help needed to update to latest fastqc
On 11/03/2015 04:09 PM, Andreas Tille wrote: > Hi Olivier, > > On Sat, 22 Aug 2015, Olivier Sallou wrote: >> ok, >> I have uploaded libsis-base-java (the first one in chain) > Any further progress on this? I have commited the latest fastqc version > to Git and fixed some issues in the packaging. Please let me know if I > can help (with my admitedly close to zero Java knowledge). For instance > trying to add the next link in chain if you simply give me an URL? sorry, I forgot to upload libsis-hdf5-java after libsis-base-java being accepted in sid. libsis-hdf5-java has just been uploaded (the one you need I think), we need to wait to get it accepted in sid. Olivier > > Kind regards > > Andreas. > -- Olivier Sallou IRISA / University of Rennes 1 Campus de Beaulieu, 35000 RENNES - FRANCE Tel: 02.99.84.71.95 gpg key id: 4096R/326D8438 (keyring.debian.org) Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438
Re: Help needed to update to latest fastqc
As libsis-base-java and libsis-jhdf5-java are in our git repo and seem to be fine, you may want to build/install them locally to test your fastqc update ? As it makes use of the libraries, it would also be a good additional test for those libs before uploading them Olivier Le lun. 4 mai 2015 à 09:04, Olivier Sallou olivier.sal...@irisa.fr a écrit : Forwarded Message Subject: Help needed to update to latest fastqc Resent-Date: Sun, 3 May 2015 06:54:37 + (UTC) Resent-From: debian-med@lists.debian.org Date: Sun, 3 May 2015 08:54:22 +0200 From: Andreas Tille andr...@an3as.eu andr...@an3as.eu To: Debian Med Project List debian-med@lists.debian.org debian-med@lists.debian.org Hi, I tried to upgrade to the latest fasqc version. When doing so I decided to move from SVN to Git: Vcs-Git: git://anonscm.debian.org/debian-med/fastqc.git Upstream needs a new Build-Depends libjhdf5-java which I added. However, I was not able to fix the build. When trying I considered switching from the Makefile based build to ant (which sounds natural) Unfortunately I did not succeeded in adapting build.xml. Any help would be appreciated Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/20150503065422.gh5...@an3as.eu
Re: Help needed to update to latest fastqc
Hi, On Sat, Aug 22, 2015 at 08:27:39AM +, olivier sallou wrote: As libsis-base-java and libsis-jhdf5-java are in our git repo and seem to be fine, you may want to build/install them locally to test your fastqc update ? As it makes use of the libraries, it would also be a good additional test for those libs before uploading them Since I personally have bo proper test case I'd vote for starting to upload the first link in the chain of dependencies. There might be pretty much time to fix things while its hanging in the new queue (hopefully less time). Thanks for your work on this Andreas. -- http://fam-tille.de
Re: Help needed to update to latest fastqc
On 08/22/2015 03:35 PM, Andreas Tille wrote: Hi, On Sat, Aug 22, 2015 at 08:27:39AM +, olivier sallou wrote: As libsis-base-java and libsis-jhdf5-java are in our git repo and seem to be fine, you may want to build/install them locally to test your fastqc update ? As it makes use of the libraries, it would also be a good additional test for those libs before uploading them Since I personally have bo proper test case I'd vote for starting to upload the first link in the chain of dependencies. There might be pretty much time to fix things while its hanging in the new queue (hopefully less time). ok, I have uploaded libsis-base-java (the first one in chain) Thanks for your work on this Andreas. -- gpg key id: 4096R/326D8438 (keyring.debian.org) Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438
Re: Help needed to update to latest fastqc
Hi Olivier,
I'm working with your updated libsis-base package. It compiles OK but I
had to tinker with the library loading to get the self tests to pass
(sse below).
I've modified the package to build according to
https://www.debian.org/doc/packaging-manuals/java-policy/x104.html. Both
native .so libraries are JNI so they are tightly bound to the Java
wrapper and no other code should ever link to them. My impression is
that therefore they should go into /usr/lib/jni and either be
un-versioned or else named like:
libcisd-nativedata-14.12.0.so
Because the .so file has to precisely match the version of the .jar file
and they can and should be updated in lock step. The usual
considerations about major.minor.bugfix versioning don't apply.
On that topic, the Java code in libsis-base loads both these libraries
on a best-effort basis and tries to fall back to native routines the
code is unavailable. I'd advocate bypassing all this with a direct call
to eg. System.loadLibrary(cisd_unix);, on the assumption that all
Debian users expect to have the native libraries loaded. The result is
that you then get an informative no such native library error right
away rather than a cryptic failure later on.
What do you think? I've committed my simplified build so you can see
what I've done. If you think I've messed it up then just revert to
r19959 which was your last version.
Cheers,
TIM
On Sun, 2015-08-16 at 17:20 +0200, olivier.sal...@codeless.fr wrote:
On 08/14/2015 10:48 AM, Tim Booth wrote:
Hi Olivier,
http://anonscm.debian.org/viewvc/debian-med/trunk/packages/libsis-base-java/
http://anonscm.debian.org/viewvc/debian-med/trunk/packages/libsis-jhdf5-java/
I've not modified FastQC at all. Or rather, I tried patching out the
FAST5 support but I just did that within the vanilla source; I'm not
playing with the package from GIT at this point.
Ok, libsis-base-java sounds good (except a few remaining polishing).
However, you can take code from svn and build package. autotests are fine.
I have updated libsis-jhdf5-java in svn too to generate native libs,
java lib (what you already did) and launch tests.
Libraries compilation is ok (.so and .jar), but tests fail when using
native libs (load is ok). I don't know why and am struggling with it, as
error message does not help (failed to instanciate). If you want to have
a look I gonna continue ot investiguate.
Olivier
Cheers,
TIM
On Fri, 2015-08-14 at 08:16 +0200, olivier.sal...@codeless.fr wrote:
On 08/13/2015 05:20 PM, Tim Booth wrote:
Hi Olivier,
Looks like Bernd Rinn is making positive noises regarding a DFSG version
of the library, so hopefully once he provides code you can take what I
have done and make use of it. I committed to SVN because it's so much
easier than pushing to GIT and I'm lazy, sorry.
what do you mean by commit to SVN ?
I looked at SVN repo for fastqc but it is empty, referring to git repo
[0]
Where is you code ?
[0] http://anonscm.debian.org/viewvc/debian-med/trunk/packages/fastqc/
Olivier
In my libsis-jhdf5-java package I created a small test
ReadWriteTest.java which I confirmed works correctly when used with
the binary libhdf5.so supplied by upstream. Also my patches
fix_dodgy_cast.patch and remove_ch_rinn_imports.patch should be sound
but the others are junk caused by me trying to kick the code into
submission.
If for some reason we can't get this working then you could very easily
patch out FAST5 support in FastQC for now. My impression is that it's
something of an alpha feature in any case. I can't even find a .fast5
format file to test with!
PATCH for FASTQC
This patch disables support for FAST5 format until we get the library
built.
Most users won't need this anyway, and those that do can convert the file
to FASTQ using other tools.
Note you also need to completely remove the file
uk/ac/babraham/FastQC/Sequence/Fast5File.java, which I can't do in a
quilt patch.
Tim Booth - 13th Aug 2015
--- a/uk/ac/babraham/FastQC/Sequence/SequenceFactory.java
+++ b/uk/ac/babraham/FastQC/Sequence/SequenceFactory.java
@@ -100,7 +100,8 @@
return new BAMFile(file,false);
}
else if (file.getName().toLowerCase().endsWith(.fast5)) {
- return new Fast5File(file);
+ //return new Fast5File(file);
+ throw new SequenceFormatException(Support for FAST5
files has not been enabled in this build of FastQC.);
}
else {
return new FastQFile(config,file);
PATCH
I'm done with this for now. Off to debug some Python code.
Best,
TIM
--
gpg key id: 4096R/326D8438 (keyring.debian.org)
Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438
--
Nothing is inherently mysterious - nothing that actually exists, that
is. If I am ignorant about a phenomenon,
Re: Help needed to update to latest fastqc
On 08/14/2015 10:48 AM, Tim Booth wrote:
Hi Olivier,
http://anonscm.debian.org/viewvc/debian-med/trunk/packages/libsis-base-java/
http://anonscm.debian.org/viewvc/debian-med/trunk/packages/libsis-jhdf5-java/
I've not modified FastQC at all. Or rather, I tried patching out the
FAST5 support but I just did that within the vanilla source; I'm not
playing with the package from GIT at this point.
Ok, libsis-base-java sounds good (except a few remaining polishing).
However, you can take code from svn and build package. autotests are fine.
I have updated libsis-jhdf5-java in svn too to generate native libs,
java lib (what you already did) and launch tests.
Libraries compilation is ok (.so and .jar), but tests fail when using
native libs (load is ok). I don't know why and am struggling with it, as
error message does not help (failed to instanciate). If you want to have
a look I gonna continue ot investiguate.
Olivier
Cheers,
TIM
On Fri, 2015-08-14 at 08:16 +0200, olivier.sal...@codeless.fr wrote:
On 08/13/2015 05:20 PM, Tim Booth wrote:
Hi Olivier,
Looks like Bernd Rinn is making positive noises regarding a DFSG version
of the library, so hopefully once he provides code you can take what I
have done and make use of it. I committed to SVN because it's so much
easier than pushing to GIT and I'm lazy, sorry.
what do you mean by commit to SVN ?
I looked at SVN repo for fastqc but it is empty, referring to git repo
[0]
Where is you code ?
[0] http://anonscm.debian.org/viewvc/debian-med/trunk/packages/fastqc/
Olivier
In my libsis-jhdf5-java package I created a small test
ReadWriteTest.java which I confirmed works correctly when used with
the binary libhdf5.so supplied by upstream. Also my patches
fix_dodgy_cast.patch and remove_ch_rinn_imports.patch should be sound
but the others are junk caused by me trying to kick the code into
submission.
If for some reason we can't get this working then you could very easily
patch out FAST5 support in FastQC for now. My impression is that it's
something of an alpha feature in any case. I can't even find a .fast5
format file to test with!
PATCH for FASTQC
This patch disables support for FAST5 format until we get the library built.
Most users won't need this anyway, and those that do can convert the file
to FASTQ using other tools.
Note you also need to completely remove the file
uk/ac/babraham/FastQC/Sequence/Fast5File.java, which I can't do in a quilt
patch.
Tim Booth - 13th Aug 2015
--- a/uk/ac/babraham/FastQC/Sequence/SequenceFactory.java
+++ b/uk/ac/babraham/FastQC/Sequence/SequenceFactory.java
@@ -100,7 +100,8 @@
return new BAMFile(file,false);
}
else if (file.getName().toLowerCase().endsWith(.fast5)) {
- return new Fast5File(file);
+ //return new Fast5File(file);
+ throw new SequenceFormatException(Support for FAST5
files has not been enabled in this build of FastQC.);
}
else {
return new FastQFile(config,file);
PATCH
I'm done with this for now. Off to debug some Python code.
Best,
TIM
--
gpg key id: 4096R/326D8438 (keyring.debian.org)
Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438
--
gpg key id: 4096R/326D8438 (keyring.debian.org)
Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438
Re: Help needed to update to latest fastqc
I am starting csid base packaging from your work. I could build native libs,
adding some autotools script to avoid using upstream scripts (one per arch).
I am adding auto test to check cisd java with native libs. Still need some
patching.
I am quite confident to get package soon. Once ready i will look at jhfd5
package. I won t focus immediatly on polishing ( control desc ...).
Oliviet
Envoyé depuis mon smartphone Sony Xperia™ via le réseau SFR
Tim Booth a écrit
Hi Olivier,
Looks like Bernd Rinn is making positive noises regarding a DFSG version
of the library, so hopefully once he provides code you can take what I
have done and make use of it. I committed to SVN because it's so much
easier than pushing to GIT and I'm lazy, sorry.
In my libsis-jhdf5-java package I created a small test
ReadWriteTest.java which I confirmed works correctly when used with
the binary libhdf5.so supplied by upstream. Also my patches
fix_dodgy_cast.patch and remove_ch_rinn_imports.patch should be sound
but the others are junk caused by me trying to kick the code into
submission.
If for some reason we can't get this working then you could very easily
patch out FAST5 support in FastQC for now. My impression is that it's
something of an alpha feature in any case. I can't even find a .fast5
format file to test with!
PATCH for FASTQC
This patch disables support for FAST5 format until we get the library built.
Most users won't need this anyway, and those that do can convert the file
to FASTQ using other tools.
Note you also need to completely remove the file
uk/ac/babraham/FastQC/Sequence/Fast5File.java, which I can't do in a quilt
patch.
Tim Booth - 13th Aug 2015
--- a/uk/ac/babraham/FastQC/Sequence/SequenceFactory.java
+++ b/uk/ac/babraham/FastQC/Sequence/SequenceFactory.java
@@ -100,7 +100,8 @@
return new BAMFile(file,false);
}
else if (file.getName().toLowerCase().endsWith(.fast5)) {
- return new Fast5File(file);
+ //return new Fast5File(file);
+ throw new SequenceFormatException(Support for FAST5
files has not been enabled in this build of FastQC.);
}
else {
return new FastQFile(config,file);
PATCH
I'm done with this for now. Off to debug some Python code.
Best,
TIM
Re: Help needed to update to latest fastqc
On 08/13/2015 05:20 PM, Tim Booth wrote:
Hi Olivier,
Looks like Bernd Rinn is making positive noises regarding a DFSG version
of the library, so hopefully once he provides code you can take what I
have done and make use of it. I committed to SVN because it's so much
easier than pushing to GIT and I'm lazy, sorry.
what do you mean by commit to SVN ?
I looked at SVN repo for fastqc but it is empty, referring to git repo [0]
Where is you code ?
[0] http://anonscm.debian.org/viewvc/debian-med/trunk/packages/fastqc/
Olivier
In my libsis-jhdf5-java package I created a small test
ReadWriteTest.java which I confirmed works correctly when used with
the binary libhdf5.so supplied by upstream. Also my patches
fix_dodgy_cast.patch and remove_ch_rinn_imports.patch should be sound
but the others are junk caused by me trying to kick the code into
submission.
If for some reason we can't get this working then you could very easily
patch out FAST5 support in FastQC for now. My impression is that it's
something of an alpha feature in any case. I can't even find a .fast5
format file to test with!
PATCH for FASTQC
This patch disables support for FAST5 format until we get the library built.
Most users won't need this anyway, and those that do can convert the file
to FASTQ using other tools.
Note you also need to completely remove the file
uk/ac/babraham/FastQC/Sequence/Fast5File.java, which I can't do in a quilt
patch.
Tim Booth - 13th Aug 2015
--- a/uk/ac/babraham/FastQC/Sequence/SequenceFactory.java
+++ b/uk/ac/babraham/FastQC/Sequence/SequenceFactory.java
@@ -100,7 +100,8 @@
return new BAMFile(file,false);
}
else if (file.getName().toLowerCase().endsWith(.fast5)) {
- return new Fast5File(file);
+ //return new Fast5File(file);
+ throw new SequenceFormatException(Support for FAST5
files has not been enabled in this build of FastQC.);
}
else {
return new FastQFile(config,file);
PATCH
I'm done with this for now. Off to debug some Python code.
Best,
TIM
--
gpg key id: 4096R/326D8438 (keyring.debian.org)
Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438
Re: Help needed to update to latest fastqc
Hi Olivier,
http://anonscm.debian.org/viewvc/debian-med/trunk/packages/libsis-base-java/
http://anonscm.debian.org/viewvc/debian-med/trunk/packages/libsis-jhdf5-java/
I've not modified FastQC at all. Or rather, I tried patching out the
FAST5 support but I just did that within the vanilla source; I'm not
playing with the package from GIT at this point.
Cheers,
TIM
On Fri, 2015-08-14 at 08:16 +0200, olivier.sal...@codeless.fr wrote:
On 08/13/2015 05:20 PM, Tim Booth wrote:
Hi Olivier,
Looks like Bernd Rinn is making positive noises regarding a DFSG version
of the library, so hopefully once he provides code you can take what I
have done and make use of it. I committed to SVN because it's so much
easier than pushing to GIT and I'm lazy, sorry.
what do you mean by commit to SVN ?
I looked at SVN repo for fastqc but it is empty, referring to git repo
[0]
Where is you code ?
[0] http://anonscm.debian.org/viewvc/debian-med/trunk/packages/fastqc/
Olivier
In my libsis-jhdf5-java package I created a small test
ReadWriteTest.java which I confirmed works correctly when used with
the binary libhdf5.so supplied by upstream. Also my patches
fix_dodgy_cast.patch and remove_ch_rinn_imports.patch should be sound
but the others are junk caused by me trying to kick the code into
submission.
If for some reason we can't get this working then you could very easily
patch out FAST5 support in FastQC for now. My impression is that it's
something of an alpha feature in any case. I can't even find a .fast5
format file to test with!
PATCH for FASTQC
This patch disables support for FAST5 format until we get the library built.
Most users won't need this anyway, and those that do can convert the file
to FASTQ using other tools.
Note you also need to completely remove the file
uk/ac/babraham/FastQC/Sequence/Fast5File.java, which I can't do in a quilt
patch.
Tim Booth - 13th Aug 2015
--- a/uk/ac/babraham/FastQC/Sequence/SequenceFactory.java
+++ b/uk/ac/babraham/FastQC/Sequence/SequenceFactory.java
@@ -100,7 +100,8 @@
return new BAMFile(file,false);
}
else if (file.getName().toLowerCase().endsWith(.fast5)) {
- return new Fast5File(file);
+ //return new Fast5File(file);
+ throw new SequenceFormatException(Support for FAST5
files has not been enabled in this build of FastQC.);
}
else {
return new FastQFile(config,file);
PATCH
I'm done with this for now. Off to debug some Python code.
Best,
TIM
--
gpg key id: 4096R/326D8438 (keyring.debian.org)
Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438
--
Nothing is inherently mysterious - nothing that actually exists, that
is. If I am ignorant about a phenomenon, that is a fact about my state
of mind, not a fact about the phenomenon; to worship a phenomenon
because it seems so wonderfully mysterious, is to worship your own
ignorance.
- Eliezer Yudkowsky
Re: Help needed to update to latest fastqc
On 08/12/2015 08:43 PM, Tim Booth wrote: Hi, After a fair amount of struggling I conclude that I do not have all the code required to build this thing from source. The distribution of JHDF5 from https://wiki-bsse.ethz.ch/pages/viewpage.action?pageId=26609113 contains some Java source code and a bunch of pre-compiled JNI shared libs, eg.: sis-jhdf5/lib/native/jhdf5/amd64-Linux/libjhdf5.so The source for this file is not to be found anywhere that I can see it. One might assume (and the FAQ implies) that the file is equivalent to /usr/lib/jni/libjhdf5.so provided by the exiting package libjhdf5-jni but it isn't! Inspecting it with readelf shows it is full of symbols in the ETH SIS namespace: tbooth@balisaur[sis-jhdf5] readelf -sW ./sis-jhdf5/lib/native/jhdf5/amd64-Linux/libjhdf5.so | grep ch_systemsx | head 19: 00039a4058 FUNCGLOBAL DEFAULT 10 Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Scopy 31: 0002e930 181 FUNCGLOBAL DEFAULT 10 Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Dchdir_1ext 35: 0003b590 918 FUNCGLOBAL DEFAULT 10 Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Sget_1select_1bounds 40: 000387f045 FUNCGLOBAL DEFAULT 10 Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pcreate_1xfer_1abort 41: 0003882066 FUNCGLOBAL DEFAULT 10 Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pget_1char_1encoding 46: 00034500 203 FUNCGLOBAL DEFAULT 10 Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Oopen 47: 00034ae0 363 FUNCGLOBAL DEFAULT 10 Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pget_1version 52: 0003521066 FUNCGLOBAL DEFAULT 10 Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pset_1layout 65: 0003c560 126 FUNCGLOBAL DEFAULT 10 Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Tget_1member_1name 68: 00032da058 FUNCGLOBAL DEFAULT 10 Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Idec_1ref ...and many more... So, this .so file is definitely specific to this library. It seems to be a superset of a fork of the upstream NCSA code. The only contact details I can find for the library are for Dr. Bernd Rinn who is the head of the whole division, but I shall contact him personally and see if he can pass the query on. I will have a look on my side. I think that I found some code some times ago, but this packaging is definitly quite hard. could you make what you made available (sis-hdf5, sis-base etc.) so that I avoid losing time doing the same thing to test compilation. Olivier If Bernd can't help, then unless I've missed a trick we will have to consider that this library and anything that depends on it (eg FastQC) are not fully open source :-( Cheers, TIM On Wed, 2015-08-12 at 15:00 +0200, Andreas Tille wrote: Hi Tim, from my *very* naive point of view your considerations make sense. Olivier might have some more educated opinion (and perhaps some code?). I'll be available vor sponsering as usual. Thanks for your work on this Andreas. On Wed, Aug 12, 2015 at 11:44:19AM +0100, Tim Booth wrote: Hi Andreas and Olivier, I'm going to have a crack at the FastQC update. I've been poking at the HDF5 packages and here are my conclusions so far: --- We have 2 Free Java libraries for HDF5: 1) The NCSA lib distributed by hdfgroup.org with classes in namespace ncsa.hdf.hdf5lib, packaged on Debian as libjhdf5-java. 2) The CISD aka. SIS lib distributed by ethz.ch with classes in the namespace ch.systemsx, not currently packaged on Debian. The SIS library forks some Java code from the ncsa.hdf namespace, and also needs to link against the NCSA native library (via JNI) at runtime. So, trying to package sis-jhdf5: wget 'https://wiki-bsse.ethz.ch/download/attachments/26609237/sis-jhdf5-14.12.1-r33502.zip?version=1modificationDate=1424599261225api=v2' # The source is in a zip within the zip... unzip sis-* mkdir sis-jhdf5-14.12.1 cd !$ unzip ../sis-jhdf5/src/sis-jhdf5-src.zip For compilation to succeed, we also need sis-base, not to be confused with the entirely separate project at sis.apache.org! wget http://bs-svn01.ethz.ch/repos/cisd/libraries/trunk/sis-base/sis-base-src.zip The code also depends on their own args4j library, but only for the CLI under ch/systemsx/cisd/hdf5/h5ar/HDF5ArchiverMain.java which we can simply leave out just now. So - can we exclude the ncsa.hdf.hdf5lib.* classes from sis-jhdf5 and compile it against the existing classes in /usr/share/java/jhdf5.jar? My conclusion is not, because... The version of ncsa/hdf/hdf5lib/exceptions/HDF5Exception.java supplied with the sis-jhdf5 code subclasses RuntimeException but the version in libhdf5-java does not. The result is that the code here does not need to declare the exceptions being thrown, and thus simply ignores them all. One can go through and add all throws declarations (there are a _lot_ of
Re: Help needed to update to latest fastqc
On 08/12/2015 12:44 PM, Tim Booth wrote: Hi Andreas and Olivier, I'm going to have a crack at the FastQC update. I've been poking at the HDF5 packages and here are my conclusions so far: I already had a look and started some work. In fact I expected to progress on it during Debconf, but if you started it... --- We have 2 Free Java libraries for HDF5: 1) The NCSA lib distributed by hdfgroup.org with classes in namespace ncsa.hdf.hdf5lib, packaged on Debian as libjhdf5-java. 2) The CISD aka. SIS lib distributed by ethz.ch with classes in the namespace ch.systemsx, not currently packaged on Debian. The SIS library forks some Java code from the ncsa.hdf namespace, and also needs to link against the NCSA native library (via JNI) at runtime. So, trying to package sis-jhdf5: wget 'https://wiki-bsse.ethz.ch/download/attachments/26609237/sis-jhdf5-14.12.1-r33502.zip?version=1modificationDate=1424599261225api=v2' # The source is in a zip within the zip... unzip sis-* mkdir sis-jhdf5-14.12.1 cd !$ unzip ../sis-jhdf5/src/sis-jhdf5-src.zip For compilation to succeed, we also need sis-base, not to be confused with the entirely separate project at sis.apache.org! Is it all ? In my previous check, it seemed (but not sure, it was quite some time ago) that there were multiple dependencies (or sis-base itself depending on other libs to package in sis repo) wget http://bs-svn01.ethz.ch/repos/cisd/libraries/trunk/sis-base/sis-base-src.zip The code also depends on their own args4j library, but only for the CLI under ch/systemsx/cisd/hdf5/h5ar/HDF5ArchiverMain.java which we can simply leave out just now. So - can we exclude the ncsa.hdf.hdf5lib.* classes from sis-jhdf5 and compile it against the existing classes in /usr/share/java/jhdf5.jar? My conclusion is not, because... The version of ncsa/hdf/hdf5lib/exceptions/HDF5Exception.java supplied with the sis-jhdf5 code subclasses RuntimeException but the version in libhdf5-java does not. The result is that the code here does not need to declare the exceptions being thrown, and thus simply ignores them all. One can go through and add all throws declarations (there are a _lot_ of them!!), but then any client code using the library will also break unless it is likewise patched or the code is modified to handle the exceptions internally. I think we'd best just admit defeat here and use the code supplied with sis-jhdf5. I think that we should indeed keep the copied code from original, as I think they adapted it for their needs. Makihng modifications to use completly nca would make it unmaintainable in later updates I think. So, I'm going to try rolling two new packages, and see if that allows me to compile the latest FastQC: libsis-base-java (should be simple) libsis-jhdf5-java (depends on libsis-base-java + existing libjhdf5-jni) I'll report back on progress and commit to SVN as usual. Let me know if you think I'm missing something. Cheers, TIM On Thu, 2015-06-25 at 09:37 +0200, Andreas Tille wrote: Hi Olivier, any news about this hdf5lib packaging? Kind regards Andreas. On Tue, May 05, 2015 at 09:25:23AM +0200, Olivier Sallou wrote: On 05/04/2015 10:52 PM, Andreas Tille wrote: Hi Olivier, On Mon, May 04, 2015 at 06:41:10PM +0200, Olivier Sallou wrote: File fastqc/uk/ac/babraham/FastQC/Sequence/Fast5File.java imports HDFS5Factory from ch.systemsx.cisd.hdf5 but jhdf5.jar only contains files like: ncsa/hdf/hdf5lib/... and no HDF5Factory this jhdf5 is not the correctl lib (or an other one is needed). I guess its this one: https://svncisd.ethz.ch/doc/hdf5/hdf5-8.10/ch/systemsx/cisd/hdf5/package-summary.html seems that original code source is the same (https://svncisd.ethz.ch/repos/cisd/jhdf5/trunk/source/java/) (/ncsa/...) but that /ch/... has not been included for a reason In addition, in debian/patches/build.xml is missing commons-math3.jar to be added in pathelement for classpath. for duplicate classes, I don't yet, but hdf5 first need to be resolved. If I do not hear from you I'll try the URL above tomorrow (if nobody else might beat me which would for sure welcome as always). Kind regards Andreas. -- Olivier Sallou IRISA / University of Rennes 1 Campus de Beaulieu, 35000 RENNES - FRANCE Tel: 02.99.84.71.95 gpg key id: 4096R/326D8438 (keyring.debian.org) Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438 -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/55487063.1090...@irisa.fr -- http://fam-tille.de -- gpg key id: 4096R/326D8438 (keyring.debian.org) Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438
Re: Help needed to update to latest fastqc
Hi Olivier,
Looks like Bernd Rinn is making positive noises regarding a DFSG version
of the library, so hopefully once he provides code you can take what I
have done and make use of it. I committed to SVN because it's so much
easier than pushing to GIT and I'm lazy, sorry.
In my libsis-jhdf5-java package I created a small test
ReadWriteTest.java which I confirmed works correctly when used with
the binary libhdf5.so supplied by upstream. Also my patches
fix_dodgy_cast.patch and remove_ch_rinn_imports.patch should be sound
but the others are junk caused by me trying to kick the code into
submission.
If for some reason we can't get this working then you could very easily
patch out FAST5 support in FastQC for now. My impression is that it's
something of an alpha feature in any case. I can't even find a .fast5
format file to test with!
PATCH for FASTQC
This patch disables support for FAST5 format until we get the library built.
Most users won't need this anyway, and those that do can convert the file
to FASTQ using other tools.
Note you also need to completely remove the file
uk/ac/babraham/FastQC/Sequence/Fast5File.java, which I can't do in a quilt
patch.
Tim Booth - 13th Aug 2015
--- a/uk/ac/babraham/FastQC/Sequence/SequenceFactory.java
+++ b/uk/ac/babraham/FastQC/Sequence/SequenceFactory.java
@@ -100,7 +100,8 @@
return new BAMFile(file,false);
}
else if (file.getName().toLowerCase().endsWith(.fast5)) {
- return new Fast5File(file);
+ //return new Fast5File(file);
+ throw new SequenceFormatException(Support for FAST5
files has not been enabled in this build of FastQC.);
}
else {
return new FastQFile(config,file);
PATCH
I'm done with this for now. Off to debug some Python code.
Best,
TIM
Re: Help needed to update to latest fastqc
Hi Andreas and Olivier, I'm going to have a crack at the FastQC update. I've been poking at the HDF5 packages and here are my conclusions so far: --- We have 2 Free Java libraries for HDF5: 1) The NCSA lib distributed by hdfgroup.org with classes in namespace ncsa.hdf.hdf5lib, packaged on Debian as libjhdf5-java. 2) The CISD aka. SIS lib distributed by ethz.ch with classes in the namespace ch.systemsx, not currently packaged on Debian. The SIS library forks some Java code from the ncsa.hdf namespace, and also needs to link against the NCSA native library (via JNI) at runtime. So, trying to package sis-jhdf5: wget 'https://wiki-bsse.ethz.ch/download/attachments/26609237/sis-jhdf5-14.12.1-r33502.zip?version=1modificationDate=1424599261225api=v2' # The source is in a zip within the zip... unzip sis-* mkdir sis-jhdf5-14.12.1 cd !$ unzip ../sis-jhdf5/src/sis-jhdf5-src.zip For compilation to succeed, we also need sis-base, not to be confused with the entirely separate project at sis.apache.org! wget http://bs-svn01.ethz.ch/repos/cisd/libraries/trunk/sis-base/sis-base-src.zip The code also depends on their own args4j library, but only for the CLI under ch/systemsx/cisd/hdf5/h5ar/HDF5ArchiverMain.java which we can simply leave out just now. So - can we exclude the ncsa.hdf.hdf5lib.* classes from sis-jhdf5 and compile it against the existing classes in /usr/share/java/jhdf5.jar? My conclusion is not, because... The version of ncsa/hdf/hdf5lib/exceptions/HDF5Exception.java supplied with the sis-jhdf5 code subclasses RuntimeException but the version in libhdf5-java does not. The result is that the code here does not need to declare the exceptions being thrown, and thus simply ignores them all. One can go through and add all throws declarations (there are a _lot_ of them!!), but then any client code using the library will also break unless it is likewise patched or the code is modified to handle the exceptions internally. I think we'd best just admit defeat here and use the code supplied with sis-jhdf5. So, I'm going to try rolling two new packages, and see if that allows me to compile the latest FastQC: libsis-base-java (should be simple) libsis-jhdf5-java (depends on libsis-base-java + existing libjhdf5-jni) I'll report back on progress and commit to SVN as usual. Let me know if you think I'm missing something. Cheers, TIM On Thu, 2015-06-25 at 09:37 +0200, Andreas Tille wrote: Hi Olivier, any news about this hdf5lib packaging? Kind regards Andreas. On Tue, May 05, 2015 at 09:25:23AM +0200, Olivier Sallou wrote: On 05/04/2015 10:52 PM, Andreas Tille wrote: Hi Olivier, On Mon, May 04, 2015 at 06:41:10PM +0200, Olivier Sallou wrote: File fastqc/uk/ac/babraham/FastQC/Sequence/Fast5File.java imports HDFS5Factory from ch.systemsx.cisd.hdf5 but jhdf5.jar only contains files like: ncsa/hdf/hdf5lib/... and no HDF5Factory this jhdf5 is not the correctl lib (or an other one is needed). I guess its this one: https://svncisd.ethz.ch/doc/hdf5/hdf5-8.10/ch/systemsx/cisd/hdf5/package-summary.html seems that original code source is the same (https://svncisd.ethz.ch/repos/cisd/jhdf5/trunk/source/java/) (/ncsa/...) but that /ch/... has not been included for a reason In addition, in debian/patches/build.xml is missing commons-math3.jar to be added in pathelement for classpath. for duplicate classes, I don't yet, but hdf5 first need to be resolved. If I do not hear from you I'll try the URL above tomorrow (if nobody else might beat me which would for sure welcome as always). Kind regards Andreas. -- Olivier Sallou IRISA / University of Rennes 1 Campus de Beaulieu, 35000 RENNES - FRANCE Tel: 02.99.84.71.95 gpg key id: 4096R/326D8438 (keyring.debian.org) Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438 -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/55487063.1090...@irisa.fr -- http://fam-tille.de -- Nothing is inherently mysterious - nothing that actually exists, that is. If I am ignorant about a phenomenon, that is a fact about my state of mind, not a fact about the phenomenon; to worship a phenomenon because it seems so wonderfully mysterious, is to worship your own ignorance. - Eliezer Yudkowsky -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/1439376259.4466.21.ca...@wllt1771.nerc-wallingford.ac.uk
Re: Help needed to update to latest fastqc
Hi Tim, from my *very* naive point of view your considerations make sense. Olivier might have some more educated opinion (and perhaps some code?). I'll be available vor sponsering as usual. Thanks for your work on this Andreas. On Wed, Aug 12, 2015 at 11:44:19AM +0100, Tim Booth wrote: Hi Andreas and Olivier, I'm going to have a crack at the FastQC update. I've been poking at the HDF5 packages and here are my conclusions so far: --- We have 2 Free Java libraries for HDF5: 1) The NCSA lib distributed by hdfgroup.org with classes in namespace ncsa.hdf.hdf5lib, packaged on Debian as libjhdf5-java. 2) The CISD aka. SIS lib distributed by ethz.ch with classes in the namespace ch.systemsx, not currently packaged on Debian. The SIS library forks some Java code from the ncsa.hdf namespace, and also needs to link against the NCSA native library (via JNI) at runtime. So, trying to package sis-jhdf5: wget 'https://wiki-bsse.ethz.ch/download/attachments/26609237/sis-jhdf5-14.12.1-r33502.zip?version=1modificationDate=1424599261225api=v2' # The source is in a zip within the zip... unzip sis-* mkdir sis-jhdf5-14.12.1 cd !$ unzip ../sis-jhdf5/src/sis-jhdf5-src.zip For compilation to succeed, we also need sis-base, not to be confused with the entirely separate project at sis.apache.org! wget http://bs-svn01.ethz.ch/repos/cisd/libraries/trunk/sis-base/sis-base-src.zip The code also depends on their own args4j library, but only for the CLI under ch/systemsx/cisd/hdf5/h5ar/HDF5ArchiverMain.java which we can simply leave out just now. So - can we exclude the ncsa.hdf.hdf5lib.* classes from sis-jhdf5 and compile it against the existing classes in /usr/share/java/jhdf5.jar? My conclusion is not, because... The version of ncsa/hdf/hdf5lib/exceptions/HDF5Exception.java supplied with the sis-jhdf5 code subclasses RuntimeException but the version in libhdf5-java does not. The result is that the code here does not need to declare the exceptions being thrown, and thus simply ignores them all. One can go through and add all throws declarations (there are a _lot_ of them!!), but then any client code using the library will also break unless it is likewise patched or the code is modified to handle the exceptions internally. I think we'd best just admit defeat here and use the code supplied with sis-jhdf5. So, I'm going to try rolling two new packages, and see if that allows me to compile the latest FastQC: libsis-base-java (should be simple) libsis-jhdf5-java (depends on libsis-base-java + existing libjhdf5-jni) I'll report back on progress and commit to SVN as usual. Let me know if you think I'm missing something. Cheers, TIM On Thu, 2015-06-25 at 09:37 +0200, Andreas Tille wrote: Hi Olivier, any news about this hdf5lib packaging? Kind regards Andreas. On Tue, May 05, 2015 at 09:25:23AM +0200, Olivier Sallou wrote: On 05/04/2015 10:52 PM, Andreas Tille wrote: Hi Olivier, On Mon, May 04, 2015 at 06:41:10PM +0200, Olivier Sallou wrote: File fastqc/uk/ac/babraham/FastQC/Sequence/Fast5File.java imports HDFS5Factory from ch.systemsx.cisd.hdf5 but jhdf5.jar only contains files like: ncsa/hdf/hdf5lib/... and no HDF5Factory this jhdf5 is not the correctl lib (or an other one is needed). I guess its this one: https://svncisd.ethz.ch/doc/hdf5/hdf5-8.10/ch/systemsx/cisd/hdf5/package-summary.html seems that original code source is the same (https://svncisd.ethz.ch/repos/cisd/jhdf5/trunk/source/java/) (/ncsa/...) but that /ch/... has not been included for a reason In addition, in debian/patches/build.xml is missing commons-math3.jar to be added in pathelement for classpath. for duplicate classes, I don't yet, but hdf5 first need to be resolved. If I do not hear from you I'll try the URL above tomorrow (if nobody else might beat me which would for sure welcome as always). Kind regards Andreas. -- Olivier Sallou IRISA / University of Rennes 1 Campus de Beaulieu, 35000 RENNES - FRANCE Tel: 02.99.84.71.95 gpg key id: 4096R/326D8438 (keyring.debian.org) Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438 -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/55487063.1090...@irisa.fr -- http://fam-tille.de -- Nothing is inherently mysterious - nothing that actually exists, that is. If I am ignorant about a phenomenon, that is a fact about my state of mind, not a fact about the phenomenon; to worship a phenomenon because it seems so wonderfully mysterious, is to worship your own ignorance. - Eliezer Yudkowsky -- http://fam-tille.de
Re: Help needed to update to latest fastqc
Hi, After a fair amount of struggling I conclude that I do not have all the code required to build this thing from source. The distribution of JHDF5 from https://wiki-bsse.ethz.ch/pages/viewpage.action?pageId=26609113 contains some Java source code and a bunch of pre-compiled JNI shared libs, eg.: sis-jhdf5/lib/native/jhdf5/amd64-Linux/libjhdf5.so The source for this file is not to be found anywhere that I can see it. One might assume (and the FAQ implies) that the file is equivalent to /usr/lib/jni/libjhdf5.so provided by the exiting package libjhdf5-jni but it isn't! Inspecting it with readelf shows it is full of symbols in the ETH SIS namespace: tbooth@balisaur[sis-jhdf5] readelf -sW ./sis-jhdf5/lib/native/jhdf5/amd64-Linux/libjhdf5.so | grep ch_systemsx | head 19: 00039a4058 FUNCGLOBAL DEFAULT 10 Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Scopy 31: 0002e930 181 FUNCGLOBAL DEFAULT 10 Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Dchdir_1ext 35: 0003b590 918 FUNCGLOBAL DEFAULT 10 Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Sget_1select_1bounds 40: 000387f045 FUNCGLOBAL DEFAULT 10 Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pcreate_1xfer_1abort 41: 0003882066 FUNCGLOBAL DEFAULT 10 Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pget_1char_1encoding 46: 00034500 203 FUNCGLOBAL DEFAULT 10 Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Oopen 47: 00034ae0 363 FUNCGLOBAL DEFAULT 10 Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pget_1version 52: 0003521066 FUNCGLOBAL DEFAULT 10 Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pset_1layout 65: 0003c560 126 FUNCGLOBAL DEFAULT 10 Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Tget_1member_1name 68: 00032da058 FUNCGLOBAL DEFAULT 10 Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Idec_1ref ...and many more... So, this .so file is definitely specific to this library. It seems to be a superset of a fork of the upstream NCSA code. The only contact details I can find for the library are for Dr. Bernd Rinn who is the head of the whole division, but I shall contact him personally and see if he can pass the query on. If Bernd can't help, then unless I've missed a trick we will have to consider that this library and anything that depends on it (eg FastQC) are not fully open source :-( Cheers, TIM On Wed, 2015-08-12 at 15:00 +0200, Andreas Tille wrote: Hi Tim, from my *very* naive point of view your considerations make sense. Olivier might have some more educated opinion (and perhaps some code?). I'll be available vor sponsering as usual. Thanks for your work on this Andreas. On Wed, Aug 12, 2015 at 11:44:19AM +0100, Tim Booth wrote: Hi Andreas and Olivier, I'm going to have a crack at the FastQC update. I've been poking at the HDF5 packages and here are my conclusions so far: --- We have 2 Free Java libraries for HDF5: 1) The NCSA lib distributed by hdfgroup.org with classes in namespace ncsa.hdf.hdf5lib, packaged on Debian as libjhdf5-java. 2) The CISD aka. SIS lib distributed by ethz.ch with classes in the namespace ch.systemsx, not currently packaged on Debian. The SIS library forks some Java code from the ncsa.hdf namespace, and also needs to link against the NCSA native library (via JNI) at runtime. So, trying to package sis-jhdf5: wget 'https://wiki-bsse.ethz.ch/download/attachments/26609237/sis-jhdf5-14.12.1-r33502.zip?version=1modificationDate=1424599261225api=v2' # The source is in a zip within the zip... unzip sis-* mkdir sis-jhdf5-14.12.1 cd !$ unzip ../sis-jhdf5/src/sis-jhdf5-src.zip For compilation to succeed, we also need sis-base, not to be confused with the entirely separate project at sis.apache.org! wget http://bs-svn01.ethz.ch/repos/cisd/libraries/trunk/sis-base/sis-base-src.zip The code also depends on their own args4j library, but only for the CLI under ch/systemsx/cisd/hdf5/h5ar/HDF5ArchiverMain.java which we can simply leave out just now. So - can we exclude the ncsa.hdf.hdf5lib.* classes from sis-jhdf5 and compile it against the existing classes in /usr/share/java/jhdf5.jar? My conclusion is not, because... The version of ncsa/hdf/hdf5lib/exceptions/HDF5Exception.java supplied with the sis-jhdf5 code subclasses RuntimeException but the version in libhdf5-java does not. The result is that the code here does not need to declare the exceptions being thrown, and thus simply ignores them all. One can go through and add all throws declarations (there are a _lot_ of them!!), but then any client code using the library will also break unless it is likewise patched or the code is modified to handle the exceptions internally. I think we'd best just admit defeat here and use the code supplied with sis-jhdf5. So, I'm going to try rolling two new
Re: Help needed to update to latest fastqc
Hi Olivier, any news about this hdf5lib packaging? Kind regards Andreas. On Tue, May 05, 2015 at 09:25:23AM +0200, Olivier Sallou wrote: On 05/04/2015 10:52 PM, Andreas Tille wrote: Hi Olivier, On Mon, May 04, 2015 at 06:41:10PM +0200, Olivier Sallou wrote: File fastqc/uk/ac/babraham/FastQC/Sequence/Fast5File.java imports HDFS5Factory from ch.systemsx.cisd.hdf5 but jhdf5.jar only contains files like: ncsa/hdf/hdf5lib/... and no HDF5Factory this jhdf5 is not the correctl lib (or an other one is needed). I guess its this one: https://svncisd.ethz.ch/doc/hdf5/hdf5-8.10/ch/systemsx/cisd/hdf5/package-summary.html seems that original code source is the same (https://svncisd.ethz.ch/repos/cisd/jhdf5/trunk/source/java/) (/ncsa/...) but that /ch/... has not been included for a reason In addition, in debian/patches/build.xml is missing commons-math3.jar to be added in pathelement for classpath. for duplicate classes, I don't yet, but hdf5 first need to be resolved. If I do not hear from you I'll try the URL above tomorrow (if nobody else might beat me which would for sure welcome as always). Kind regards Andreas. -- Olivier Sallou IRISA / University of Rennes 1 Campus de Beaulieu, 35000 RENNES - FRANCE Tel: 02.99.84.71.95 gpg key id: 4096R/326D8438 (keyring.debian.org) Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438 -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/55487063.1090...@irisa.fr -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/20150625073719.gc28...@an3as.eu
Re: Help needed to update to latest fastqc
On 05/04/2015 10:52 PM, Andreas Tille wrote: Hi Olivier, On Mon, May 04, 2015 at 06:41:10PM +0200, Olivier Sallou wrote: File fastqc/uk/ac/babraham/FastQC/Sequence/Fast5File.java imports HDFS5Factory from ch.systemsx.cisd.hdf5 but jhdf5.jar only contains files like: ncsa/hdf/hdf5lib/... and no HDF5Factory this jhdf5 is not the correctl lib (or an other one is needed). I guess its this one: https://svncisd.ethz.ch/doc/hdf5/hdf5-8.10/ch/systemsx/cisd/hdf5/package-summary.html Looks fine. However it is not clear about the difference with hdf5 lib in Debian. would mean to package an additional hdf5 lib... ? In addition, in debian/patches/build.xml is missing commons-math3.jar to be added in pathelement for classpath. for duplicate classes, I don't yet, but hdf5 first need to be resolved. If I do not hear from you I'll try the URL above tomorrow (if nobody else might beat me which would for sure welcome as always). Kind regards Andreas. -- Olivier Sallou IRISA / University of Rennes 1 Campus de Beaulieu, 35000 RENNES - FRANCE Tel: 02.99.84.71.95 gpg key id: 4096R/326D8438 (keyring.debian.org) Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438 -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/55486c86.2020...@irisa.fr
Re: Help needed to update to latest fastqc
On 05/04/2015 10:52 PM, Andreas Tille wrote: Hi Olivier, On Mon, May 04, 2015 at 06:41:10PM +0200, Olivier Sallou wrote: File fastqc/uk/ac/babraham/FastQC/Sequence/Fast5File.java imports HDFS5Factory from ch.systemsx.cisd.hdf5 but jhdf5.jar only contains files like: ncsa/hdf/hdf5lib/... and no HDF5Factory this jhdf5 is not the correctl lib (or an other one is needed). I guess its this one: https://svncisd.ethz.ch/doc/hdf5/hdf5-8.10/ch/systemsx/cisd/hdf5/package-summary.html seems that original code source is the same (https://svncisd.ethz.ch/repos/cisd/jhdf5/trunk/source/java/) (/ncsa/...) but that /ch/... has not been included for a reason In addition, in debian/patches/build.xml is missing commons-math3.jar to be added in pathelement for classpath. for duplicate classes, I don't yet, but hdf5 first need to be resolved. If I do not hear from you I'll try the URL above tomorrow (if nobody else might beat me which would for sure welcome as always). Kind regards Andreas. -- Olivier Sallou IRISA / University of Rennes 1 Campus de Beaulieu, 35000 RENNES - FRANCE Tel: 02.99.84.71.95 gpg key id: 4096R/326D8438 (keyring.debian.org) Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438 -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/55487063.1090...@irisa.fr
Missing files in libjhdf5-java (Was: Help needed to update to latest fastqc)
Hi Sylvestre, Olivier claimed below that some files are missing in the Debian packaged libjhdf5-java. I have checked the jhdf packaging and realised that we are lagging behind upstream. I took the freedom to add a Team upload entry to d/changelog and updated debian/watch to point to the new download location. I also moved to machine readable copyright and used Files-Excluded to get rid of the bundled *.jar files. Moreover I used `cme fix dpkg-control` to normalise the d/control file and update to latest Standard-Version. I hope that this might help to upgrade to the latest upsteam version which might be interesting to package. Unfortunately I can not find find any ch/... files and thus I wonder where Olivier might have found these. Olivier, are you refering to some older jhdf version? Kind regards Andreas. - Forwarded message from Olivier Sallou olivier.sal...@irisa.fr - Date: Tue, 05 May 2015 09:25:23 +0200 From: Olivier Sallou olivier.sal...@irisa.fr To: debian-med@lists.debian.org Subject: Re: Help needed to update to latest fastqc On 05/04/2015 10:52 PM, Andreas Tille wrote: Hi Olivier, On Mon, May 04, 2015 at 06:41:10PM +0200, Olivier Sallou wrote: File fastqc/uk/ac/babraham/FastQC/Sequence/Fast5File.java imports HDFS5Factory from ch.systemsx.cisd.hdf5 but jhdf5.jar only contains files like: ncsa/hdf/hdf5lib/... and no HDF5Factory this jhdf5 is not the correctl lib (or an other one is needed). I guess its this one: https://svncisd.ethz.ch/doc/hdf5/hdf5-8.10/ch/systemsx/cisd/hdf5/package-summary.html seems that original code source is the same (https://svncisd.ethz.ch/repos/cisd/jhdf5/trunk/source/java/) (/ncsa/...) but that /ch/... has not been included for a reason In addition, in debian/patches/build.xml is missing commons-math3.jar to be added in pathelement for classpath. for duplicate classes, I don't yet, but hdf5 first need to be resolved. If I do not hear from you I'll try the URL above tomorrow (if nobody else might beat me which would for sure welcome as always). Kind regards Andreas. -- Olivier Sallou IRISA / University of Rennes 1 Campus de Beaulieu, 35000 RENNES - FRANCE Tel: 02.99.84.71.95 gpg key id: 4096R/326D8438 (keyring.debian.org) Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438 -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/55487063.1090...@irisa.fr - End forwarded message - -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/20150505082120.gb...@an3as.eu
Re: Missing files in libjhdf5-java (Was: Help needed to update to latest fastqc)
On 05/05/2015 10:21 AM, Andreas Tille wrote: Hi Sylvestre, Olivier claimed below that some files are missing in the Debian packaged libjhdf5-java. I have checked the jhdf packaging and realised that we are lagging behind upstream. I took the freedom to add a Team upload entry to d/changelog and updated debian/watch to point to the new download location. I also moved to machine readable copyright and used Files-Excluded to get rid of the bundled *.jar files. Moreover I used `cme fix dpkg-control` to normalise the d/control file and update to latest Standard-Version. I hope that this might help to upgrade to the latest upsteam version which might be interesting to package. Unfortunately I can not find find any ch/... files and thus I wonder where Olivier might have found these. Olivier, are you refering to some older jhdf version? I do not know if https://svncisd.ethz.ch/repos/cisd/jhdf5 is the same source as package in Debian. Kind regards Andreas. - Forwarded message from Olivier Sallou olivier.sal...@irisa.fr - Date: Tue, 05 May 2015 09:25:23 +0200 From: Olivier Sallou olivier.sal...@irisa.fr To: debian-med@lists.debian.org Subject: Re: Help needed to update to latest fastqc On 05/04/2015 10:52 PM, Andreas Tille wrote: Hi Olivier, On Mon, May 04, 2015 at 06:41:10PM +0200, Olivier Sallou wrote: File fastqc/uk/ac/babraham/FastQC/Sequence/Fast5File.java imports HDFS5Factory from ch.systemsx.cisd.hdf5 but jhdf5.jar only contains files like: ncsa/hdf/hdf5lib/... and no HDF5Factory this jhdf5 is not the correctl lib (or an other one is needed). I guess its this one: https://svncisd.ethz.ch/doc/hdf5/hdf5-8.10/ch/systemsx/cisd/hdf5/package-summary.html seems that original code source is the same (https://svncisd.ethz.ch/repos/cisd/jhdf5/trunk/source/java/) (/ncsa/...) but that /ch/... has not been included for a reason In addition, in debian/patches/build.xml is missing commons-math3.jar to be added in pathelement for classpath. for duplicate classes, I don't yet, but hdf5 first need to be resolved. If I do not hear from you I'll try the URL above tomorrow (if nobody else might beat me which would for sure welcome as always). Kind regards Andreas. -- Olivier Sallou IRISA / University of Rennes 1 Campus de Beaulieu, 35000 RENNES - FRANCE Tel: 02.99.84.71.95 gpg key id: 4096R/326D8438 (keyring.debian.org) Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438 -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/554893e1.2030...@irisa.fr
Re: Help needed to update to latest fastqc
On 05/03/2015 08:54 AM, Andreas Tille wrote: Hi, I tried to upgrade to the latest fasqc version. When doing so I decided to move from SVN to Git: Vcs-Git: git://anonscm.debian.org/debian-med/fastqc.git Upstream needs a new Build-Depends libjhdf5-java which I added. However, I was not able to fix the build. When trying I considered switching from the Makefile based build to ant (which sounds natural) Unfortunately I did not succeeded in adapting build.xml. Any help would be appreciated I will try to have a look this week. Olivier Andreas. -- Olivier Sallou IRISA / University of Rennes 1 Campus de Beaulieu, 35000 RENNES - FRANCE Tel: 02.99.84.71.95 gpg key id: 4096R/326D8438 (keyring.debian.org) Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438 -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/554719b6.60...@irisa.fr
Re: Help needed to update to latest fastqc
After a quick look, there is a library issue (at least) File fastqc/uk/ac/babraham/FastQC/Sequence/Fast5File.java imports HDFS5Factory from ch.systemsx.cisd.hdf5 but jhdf5.jar only contains files like: ncsa/hdf/hdf5lib/... and no HDF5Factory this jhdf5 is not the correctl lib (or an other one is needed). In addition, in debian/patches/build.xml is missing commons-math3.jar to be added in pathelement for classpath. for duplicate classes, I don't yet, but hdf5 first need to be resolved. Olivier On 05/03/2015 08:54 AM, Andreas Tille wrote: Hi, I tried to upgrade to the latest fasqc version. When doing so I decided to move from SVN to Git: Vcs-Git: git://anonscm.debian.org/debian-med/fastqc.git Upstream needs a new Build-Depends libjhdf5-java which I added. However, I was not able to fix the build. When trying I considered switching from the Makefile based build to ant (which sounds natural) Unfortunately I did not succeeded in adapting build.xml. Any help would be appreciated Andreas. -- Olivier Sallou IRISA / University of Rennes 1 Campus de Beaulieu, 35000 RENNES - FRANCE Tel: 02.99.84.71.95 gpg key id: 4096R/326D8438 (keyring.debian.org) Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438
Re: Help needed to update to latest fastqc
Hi Olivier, On Mon, May 04, 2015 at 06:41:10PM +0200, Olivier Sallou wrote: File fastqc/uk/ac/babraham/FastQC/Sequence/Fast5File.java imports HDFS5Factory from ch.systemsx.cisd.hdf5 but jhdf5.jar only contains files like: ncsa/hdf/hdf5lib/... and no HDF5Factory this jhdf5 is not the correctl lib (or an other one is needed). I guess its this one: https://svncisd.ethz.ch/doc/hdf5/hdf5-8.10/ch/systemsx/cisd/hdf5/package-summary.html In addition, in debian/patches/build.xml is missing commons-math3.jar to be added in pathelement for classpath. for duplicate classes, I don't yet, but hdf5 first need to be resolved. If I do not hear from you I'll try the URL above tomorrow (if nobody else might beat me which would for sure welcome as always). Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/20150504205235.gb20...@an3as.eu
Help needed to update to latest fastqc
Hi, I tried to upgrade to the latest fasqc version. When doing so I decided to move from SVN to Git: Vcs-Git: git://anonscm.debian.org/debian-med/fastqc.git Upstream needs a new Build-Depends libjhdf5-java which I added. However, I was not able to fix the build. When trying I considered switching from the Makefile based build to ant (which sounds natural) Unfortunately I did not succeeded in adapting build.xml. Any help would be appreciated Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/20150503065422.gh5...@an3as.eu
