[Bug 597307] New: Review Request: fastx_toolkit - Tools to process short-reads FASTA/FASTQ files

[Red Hat Bugzilla]

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Summary: Review Request: fastx_toolkit - Tools to process short-reads FASTA/FASTQ files

https://bugzilla.redhat.com/show_bug.cgi?id=597307

Summary: Review Request: fastx_toolkit - Tools to process
                    short-reads FASTA/FASTQ files
           Product: Fedora
           Version: rawhide
          Platform: All
        OS/Version: Linux
            Status: NEW
          Severity: medium
          Priority: medium
         Component: Package Review
        AssignedTo: [e-mail]
        ReportedBy: [e-mail]
         QAContact: [e-mail]
                CC: [e-mail], [e-mail]
   Estimated Hours: 0.0
    Classification: Fedora

Spec URL:
http://verdurin.org.uk/~verdurin/fedora/reviews/fastx_toolkit/fastx_toolkit....
SRPM URL:
http://verdurin.org.uk/~verdurin/fedora/reviews/fastx_toolkit/fastx_toolkit-...
Description:

The FASTX-Toolkit is a collection of command line tools for
Short-Reads FASTA/FASTQ files preprocessing.

Next-Generation sequencing machines usually produce FASTA or FASTQ
files, containing multiple short-reads sequences (possibly with
quality information).

The main processing of such FASTA/FASTQ files is mapping (aka
aligning) the sequences to reference genomes or other databases using
specialized programs. Example of such mapping programs are: Blat,
SHRiMP, LastZ, MAQ and many many others.

However, It is sometimes more productive to preprocess the FASTA/FASTQ
files before mapping the sequences to the genome - manipulating the
sequences to produce better mapping results.

The FASTX-Toolkit tools perform some of these preprocessing tasks.

[Bug 597307] Review Request: fastx_toolkit - Tools to process short-reads FASTA/FASTQ files

[Red Hat Bugzilla]

Please do not reply directly to this email. All additional
comments should be made in the comments box of this bug.

https://bugzilla.redhat.com/show_bug.cgi?id=597307

Takanori MATSUURA  changed:

What    |Removed                     |Added
----------------------------------------------------------------------------
                 CC|                            |[e-mail]

--- Comment #1 from Takanori MATSUURA  2010-06-01 06:21:36 EDT ---
This is an informal review. Formal review will follow.

Critical issue:
MUST: The package MUST successfully compile and build into binary rpms.
SHOULD: The package builds in mock.
$ mock --rebuild fastx_toolkit-0.0.13-1.fc12.src.rpm
is failed because libgtextutils-devel which is set as BuildRequires is not
available by Fedora.

You should add libgtextutils-devel package to Fedora first.

Issues:
$ rpmlint fastx_toolkit.spec
fastx_toolkit.spec:8: W: mixed-use-of-spaces-and-tabs (spaces: line 1, tab:
line 8)
Please fix mixed usage of spaces and tabs.

Lists confirmed:
+ rpmlint against SRPM returns spelling-error warning. However the words
pointed by rpmlint are from official website and seem to be no problem.

+ Spec file name meets Packaging Guidelines.
+ License: AGPLv3 meets Licensing Guidelines.
+ Source file match with upstream one with md5sum and sha1sum.

MUST: The package does not yet exist in Fedora. The Review Request is not a
duplicate. OK
MUST: The spec file for the package is legible and macros are used
consistently. OK
MUST: The package must be named according to the Package Naming Guidelines. OK
MUST: The spec file name must match the base package %{name}. OK
MUST: The package must be licensed with a Fedora approved license and meet the 
Licensing Guidelines. OK
MUST: The License field in the package spec file must match the actual license.
OK
MUST: The sources used to build the package must match the upstream source, as
provided in the spec URL. OK
MUST: The spec file MUST handle locales properly. N/A
MUST: Clean section exists. OK
MUST: Large documentation files must go in a -doc subpackage. N/A
MUST: Buildroot cleaned before install. OK
SHOULD: %{?dist} tag is used in release. OK
SHOULD: If the package does not include license text(s) as separate files from
upstream, the packager should query upstream to include it. OK

The following item will be checked after the critical issue is solved.
MUST: Optflags are used and time stamps preserved.
MUST: Packages containing shared library files must call ldconfig.
MUST: A package must own all directories that it creates or require the package
that owns the directory.
MUST: Files only listed once in %files listings.
MUST: Debuginfo package is complete.
MUST: Permissions on files must be set properly.
MUST: All relevant items are included in %doc. Items in %doc do not affect
runtime of application.
MUST: Header files must be in a -devel package.
MUST: Static libraries must be in a -static package.
MUST: Packages containing pkgconfig(.pc) files must 'Requires: pkgconfig'.
MUST: If a package contains library files with a suffix then library files
ending in .so must go in a -devel package.
MUST: In the vast majority of cases, devel packages must require the base
package using a fully versioned dependency.
MUST: Packages does not contain any .la libtool archives.
MUST: Desktop files are installed properly.
MUST: No file conflicts with other packages and no general names.

[Bug 597307] Review Request: fastx_toolkit - Tools to process short-reads FASTA/FASTQ files

[Red Hat Bugzilla]

Please do not reply directly to this email. All additional
comments should be made in the comments box of this bug.

https://bugzilla.redhat.com/show_bug.cgi?id=597307

--- Comment #2 from Adam Huffman  2010-06-01 10:34:29 EDT ---
(In reply to comment #1)
> This is an informal review. Formal review will follow.

Thanks for taking a look.
> Critical issue:
> MUST: The package MUST successfully compile and build into binary rpms.
> SHOULD: The package builds in mock.
> $ mock --rebuild fastx_toolkit-0.0.13-1.fc12.src.rpm
> is failed because libgtextutils-devel which is set as BuildRequires is not
> available by Fedora.
>
> You should add libgtextutils-devel package to Fedora first.

Yes, that's right.  I uploaded a bunch of new requests late on Friday, after
having installed them locally.  The request for libgtextutils is at:

https://bugzilla.redhat.com/show_bug.cgi?id=598511
> Issues:
> $ rpmlint fastx_toolkit.spec
> fastx_toolkit.spec:8: W: mixed-use-of-spaces-and-tabs (spaces: line 1, tab:
> line 8)
> Please fix mixed usage of spaces and tabs.

Will take a look at that.
> Lists confirmed:
> rpmlint against SRPM returns spelling-error warning. However the words
>
> pointed by rpmlint are from official website and seem to be no problem.
> Spec file name meets Packaging Guidelines.
> License: AGPLv3 meets Licensing Guidelines.
> Source file match with upstream one with md5sum and sha1sum.
>
> MUST: The package does not yet exist in Fedora. The Review Request is not a
> duplicate. OK
> MUST: The spec file for the package is legible and macros are used
> consistently. OK
> MUST: The package must be named according to the Package Naming Guidelines. OK
> MUST: The spec file name must match the base package %{name}. OK
> MUST: The package must be licensed with a Fedora approved license and meet the 
> Licensing Guidelines. OK
> MUST: The License field in the package spec file must match the actual license.
> OK
> MUST: The sources used to build the package must match the upstream source, as
> provided in the spec URL. OK
> MUST: The spec file MUST handle locales properly. N/A
> MUST: Clean section exists. OK
> MUST: Large documentation files must go in a -doc subpackage. N/A
> MUST: Buildroot cleaned before install. OK
> SHOULD: %{?dist} tag is used in release. OK
> SHOULD: If the package does not include license text(s) as separate files from
> upstream, the packager should query upstream to include it. OK
>
> The following item will be checked after the critical issue is solved.
> MUST: Optflags are used and time stamps preserved.
> MUST: Packages containing shared library files must call ldconfig.
> MUST: A package must own all directories that it creates or require the package
> that owns the directory.
> MUST: Files only listed once in %files listings.
> MUST: Debuginfo package is complete.
> MUST: Permissions on files must be set properly.
> MUST: All relevant items are included in %doc. Items in %doc do not affect
> runtime of application.
> MUST: Header files must be in a -devel package.
> MUST: Static libraries must be in a -static package.
> MUST: Packages containing pkgconfig(.pc) files must 'Requires: pkgconfig'.
> MUST: If a package contains library files with a suffix then library files
> ending in .so must go in a -devel package.
> MUST: In the vast majority of cases, devel packages must require the base
> package using a fully versioned dependency.
> MUST: Packages does not contain any .la libtool archives.
> MUST: Desktop files are installed properly.
> MUST: No file conflicts with other packages and no general names.

[Bug 597307] Review Request: fastx_toolkit - Tools to process short-reads FASTA/FASTQ files

[Red Hat Bugzilla]

Please do not reply directly to this email. All additional
comments should be made in the comments box of this bug.

https://bugzilla.redhat.com/show_bug.cgi?id=597307

Adam Huffman  changed:

What    |Removed                     |Added
----------------------------------------------------------------------------
         Depends on|                            |598511

[Bug 597307] Review Request: fastx_toolkit - Tools to process short-reads FASTA/FASTQ files

[Red Hat Bugzilla]

Please do not reply directly to this email. All additional
comments should be made in the comments box of this bug.

https://bugzilla.redhat.com/show_bug.cgi?id=597307

--- Comment #3 from Michael Schwendt  2010-06-21 05:52:45 EDT ---
> MUST: Optflags are used and time stamps preserved.

Not entirely. The source code overrides Fedora's optflags.

* Description of the -devel subpackage doesn't match its contents:

| The fastx_toolkit-devel package contains libraries and
| header files for developing applications that use fastx_toolkit.

It doesn't contain any libraries and header files.

It contains two M4 macro definition files from the GNU Autoconf Archive. It's
questionable to assign them to this package and place them in the public
aclocal directory.

$ rpmls -p fastx_toolkit-devel-0.0.13-1.fc13.x86_64.rpm|grep local
-rw-r--r--  /usr/share/aclocal/ax_c_long_long.m4
-rw-r--r--  /usr/share/aclocal/ax_cxx_header_stdcxx_tr1.m4

The only other contents of the -devel package is the big tree at:
/usr/share/doc/fastx_toolkit-devel-0.0.13/galaxy

Licensed differently (!).
Lots of unusable Makefile* files.
Icon files, XML files, not really any documentation about all that.
Strange place to dump that into %doc and a -devel pkg.

[Bug 597307] Review Request: fastx_toolkit - Tools to process short-reads FASTA/FASTQ files

[Red Hat Bugzilla]

Please do not reply directly to this email. All additional
comments should be made in the comments box of this bug.

https://bugzilla.redhat.com/show_bug.cgi?id=597307

--- Comment #4 from Adam Huffman  2010-06-21 06:29:52 EDT ---
Thanks for taking a look.  Yes, the description is a bit generic - I thought
I'd put in a note to this bug about the Galaxy files but clearly forgot. 
They're for integrating the package with a local Galaxy installation.  I wasn't
quite sure how to handle them.  Perhaps a different subpackage -
fastx_toolkit-galaxy?

Would you recommend not packaging the M4 files?

[Bug 597307] Review Request: fastx_toolkit - Tools to process short-reads FASTA/FASTQ files

[Red Hat Bugzilla]

Please do not reply directly to this email. All additional
comments should be made in the comments box of this bug.

https://bugzilla.redhat.com/show_bug.cgi?id=597307

--- Comment #5 from Michael Schwendt  2010-06-21 07:49:49 EDT ---
> Would you recommend not packaging the M4 files?

Yes.

Those two files either belong into a comprehensive autoconf-archive package
(for the scripts included in the GNU Autoconf Archive) or into the local
autotools build framework of software that wants to use these macros (e.g. in a
local "m4" subdir).

If more packages started placing arbitrary M4 files from the Autoconf Archive
into /usr/share/aclocal, this would increase the risk of causing conflicts.

[Bug 597307] Review Request: fastx_toolkit - Tools to process short-reads FASTA/FASTQ files

[Red Hat Bugzilla]

Please do not reply directly to this email. All additional
comments should be made in the comments box of this bug.

https://bugzilla.redhat.com/show_bug.cgi?id=597307

Jussi Lehtola  changed:

What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|NEW                         |ASSIGNED
                 CC|                            |[e-mail]
         AssignedTo|[e-mail]    |[e-mail]
               Flag|                            |fedora-review?

[Bug 597307] Review Request: fastx_toolkit - Tools to process short-reads FASTA/FASTQ files

[Red Hat Bugzilla]

Please do not reply directly to this email. All additional
comments should be made in the comments box of this bug.

https://bugzilla.redhat.com/show_bug.cgi?id=597307

--- Comment #6 from Jussi Lehtola  2010-08-24 12:58:07 EDT ---
rpmlint output:
fastx_toolkit.src: W: spelling-error %description -l en_US preprocessing ->
reprocessing, p reprocessing, preprocessed
fastx_toolkit.src: W: spelling-error %description -l en_US preprocess ->
reprocess, p reprocess, processors
fastx_toolkit.src:8: W: mixed-use-of-spaces-and-tabs (spaces: line 1, tab: line
8)
fastx_toolkit.x86_64: W: spelling-error %description -l en_US preprocessing ->
reprocessing, p reprocessing, preprocessed
fastx_toolkit.x86_64: W: spelling-error %description -l en_US preprocess ->
reprocess, p reprocess, processors
fastx_toolkit.x86_64: W: no-manual-page-for-binary fasta_clipping_histogram.pl
fastx_toolkit.x86_64: W: no-manual-page-for-binary fastq_quality_trimmer
fastx_toolkit.x86_64: W: no-manual-page-for-binary fastx_quality_stats
fastx_toolkit.x86_64: W: no-manual-page-for-binary fastq_quality_filter
fastx_toolkit.x86_64: W: no-manual-page-for-binary fastx_trimmer
fastx_toolkit.x86_64: W: no-manual-page-for-binary
fastq_quality_boxplot_graph.sh
fastx_toolkit.x86_64: W: no-manual-page-for-binary fastx_barcode_splitter.pl
fastx_toolkit.x86_64: W: no-manual-page-for-binary fastq_quality_converter
fastx_toolkit.x86_64: W: no-manual-page-for-binary
fastx_nucleotide_distribution_line_graph.sh
fastx_toolkit.x86_64: W: no-manual-page-for-binary fasta_formatter
fastx_toolkit.x86_64: W: no-manual-page-for-binary fastx_collapser
fastx_toolkit.x86_64: W: no-manual-page-for-binary fastx_renamer
fastx_toolkit.x86_64: W: no-manual-page-for-binary fasta_nucleotide_changer
fastx_toolkit.x86_64: W: no-manual-page-for-binary fastx_reverse_complement
fastx_toolkit.x86_64: W: no-manual-page-for-binary fastq_to_fasta
fastx_toolkit.x86_64: W: no-manual-page-for-binary
fastx_nucleotide_distribution_graph.sh
fastx_toolkit.x86_64: W: no-manual-page-for-binary fastq_masker
fastx_toolkit.x86_64: W: no-manual-page-for-binary fastx_artifacts_filter
fastx_toolkit.x86_64: W: no-manual-page-for-binary fastx_uncollapser
fastx_toolkit.x86_64: W: no-manual-page-for-binary fastx_clipper
fastx_toolkit-debuginfo.x86_64: W: spelling-error Summary(en_US) fastx -> fast,
fasts, fast x
fastx_toolkit-debuginfo.x86_64: W: spelling-error %description -l en_US fastx
-> fast, fasts, fast x
fastx_toolkit-devel.x86_64: W: spelling-error Summary(en_US) fastx -> fast,
fasts, fast x
fastx_toolkit-devel.x86_64: W: spelling-error %description -l en_US fastx ->
fast, fasts, fast x
fastx_toolkit-devel.x86_64: W: spurious-executable-perm
/usr/share/doc/fastx_toolkit-devel-0.0.13/galaxy/tools/fastx_toolkit/fastx_barcode_splitter_galaxy_wrapper.sh
4 packages and 0 specfiles checked; 0 errors, 30 warnings.

- Check your tabs vs spaces.

- Placing the galaxy stuff somewhere else than %doc gets rid of the exec perm
warning. When packaging the galaxy stuff, be sure not to include any Makefiles
or the like.

- Please use
 http://hannonlab.cshl.edu/fastx_toolkit/
as the URL. It's nicer not to have macros in the URL, so one can cut'n'paste
from the spec.

- Don't ship the m4 files, as instructed by Michael.

**

MUST: The package does not yet exist in Fedora. The Review Request is not a
duplicate. OK
MUST: The spec file for the package is legible and macros are used
consistently. OK
MUST: The package must be named according to the Package Naming Guidelines. OK
MUST: The spec file name must match the base package %{name}. OK
MUST: The package must be licensed with a Fedora approved license and meet the 
Licensing Guidelines. OK

MUST: The License field in the package spec file must match the actual license.
NEEDSWORK
- License is AGPLv3+, not AGPLv3.

MUST: The sources used to build the package must match the upstream source, as
provided in the spec URL. OK
6d233ff4ae3d52c457d447179f073a56  fastx_toolkit-0.0.13.tar.bz2
6d233ff4ae3d52c457d447179f073a56  ../SOURCES/fastx_toolkit-0.0.13.tar.bz2

MUST: The package MUST successfully compile and build into binary rpms. OK
MUST: The spec file MUST handle locales properly. N/A

MUST: Optflags are used and time stamps preserved. NEEDSWORK
- As already pointed out by Michael, the build process overrides the Fedora
optimization flags.
- Use
 make %{?_smp_mflags} CFLAGS="$RPM_OPT_FLAGS" CXXFLAGS="$RPM_OPT_FLAGS"
to correct this.
- Also, please use
 make install INSTALL="install -p"
to keep the time stamps in %install.

MUST: Packages containing shared library files must call ldconfig. N/A
MUST: A package must own all directories that it creates or require the package
that owns the directory. OK

MUST: Files only listed once in %files listings. OK
- Maybe again make things a bit more verbose with
 %{_bindir}/fast*
?

MUST: Debuginfo package is complete. OK
MUST: Permissions on files must be set properly. OK
MUST: Large documentation files must go in a -doc subpackage. N/A
MUST: All relevant items are included in %doc. Items in %doc do not affect
runtime of application. OK
MUST: Header files must be in a -devel package. N/A
MUST: Static libraries must be in a -static package. N/A
MUST: If a package contains library files with a suffix then library files
ending in .so must go in a -devel package. N/A
MUST: In the vast majority of cases, devel packages must require the base
package using a fully versioned dependency. N/A
MUST: Packages does not contain any .la libtool archives. N/A
MUST: Desktop files are installed properly. N/A
MUST: No file conflicts with other packages and no general names. OK
SHOULD: %{?dist} tag is used in release. OK
SHOULD: If the package does not include license text(s) as separate files from
upstream, the packager should query upstream to include it. OK
SHOULD: The package builds in mock. OK
EPEL: Clean section exists. OK
EPEL: Buildroot cleaned before install. OK
EPEL: Packages containing pkgconfig(.pc) files must 'Requires: pkgconfig'. N/A

[Bug 597307] Review Request: fastx_toolkit - Tools to process short-reads FASTA/FASTQ files

[Red Hat Bugzilla]

Please do not reply directly to this email. All additional
comments should be made in the comments box of this bug.

https://bugzilla.redhat.com/show_bug.cgi?id=597307

--- Comment #7 from Chen Lei  2010-08-24 20:59:49 EDT ---
I'm sure that galaxy is not for development purpose, and m4 macros is
completely useless for this package.

[Bug 597307] Review Request: fastx_toolkit - Tools to process short-reads FASTA/FASTQ files

[Red Hat Bugzilla]

Please do not reply directly to this email. All additional
comments should be made in the comments box of this bug.

https://bugzilla.redhat.com/show_bug.cgi?id=597307

--- Comment #8 from Adam Huffman  2010-08-25 12:23:18 EDT ---
New version at:

http://verdurin.org.uk/~verdurin/fedora/reviews/fastx_toolkit/fastx_toolkit....

http://verdurin.org.uk/~verdurin/fedora/reviews/fastx_toolkit/fastx_toolkit-...

As with libgtextutils, there's no apparent acceptable license tag "AGPLv3+".

I've made a -galaxy subpackage for the galaxy/ directory.

[Bug 597307] Review Request: fastx_toolkit - Tools to process short-reads FASTA/FASTQ files

[Red Hat Bugzilla]

Please do not reply directly to this email. All additional
comments should be made in the comments box of this bug.

https://bugzilla.redhat.com/show_bug.cgi?id=597307

--- Comment #9 from Jussi Lehtola  2010-11-06 09:15:11 EDT ---
Whoops, I'm terribly sorry that this has slipped under my radar, as I've been
quite busy at $DAYJOB. I'll try to look through this ASAP.

[Bug 597307] Review Request: fastx_toolkit - Tools to process short-reads FASTA/FASTQ files

[Red Hat Bugzilla]

Please do not reply directly to this email. All additional
comments should be made in the comments box of this bug.

https://bugzilla.redhat.com/show_bug.cgi?id=597307

--- Comment #10 from Jussi Lehtola  2010-11-07 04:41:14 EST ---
rpmlint output now at:

fastx_toolkit.src: W: spelling-error %description -l en_US preprocessing ->
reprocessing, p reprocessing, preprocessed
fastx_toolkit.src: W: spelling-error %description -l en_US preprocess ->
reprocess, p reprocess, procession
fastx_toolkit.x86_64: W: spelling-error %description -l en_US preprocessing ->
reprocessing, p reprocessing, preprocessed
fastx_toolkit.x86_64: W: spelling-error %description -l en_US preprocess ->
reprocess, p reprocess, procession
fastx_toolkit.x86_64: W: no-manual-page-for-binary fasta_clipping_histogram.pl
fastx_toolkit.x86_64: W: no-manual-page-for-binary fastq_quality_trimmer
fastx_toolkit.x86_64: W: no-manual-page-for-binary fastx_quality_stats
fastx_toolkit.x86_64: W: no-manual-page-for-binary fastq_quality_filter
fastx_toolkit.x86_64: W: no-manual-page-for-binary fastx_trimmer
fastx_toolkit.x86_64: W: no-manual-page-for-binary
fastq_quality_boxplot_graph.sh
fastx_toolkit.x86_64: W: no-manual-page-for-binary fastx_barcode_splitter.pl
fastx_toolkit.x86_64: W: no-manual-page-for-binary fastq_quality_converter
fastx_toolkit.x86_64: W: no-manual-page-for-binary
fastx_nucleotide_distribution_line_graph.sh
fastx_toolkit.x86_64: W: no-manual-page-for-binary fasta_formatter
fastx_toolkit.x86_64: W: no-manual-page-for-binary fastx_collapser
fastx_toolkit.x86_64: W: no-manual-page-for-binary fastx_renamer
fastx_toolkit.x86_64: W: no-manual-page-for-binary fasta_nucleotide_changer
fastx_toolkit.x86_64: W: no-manual-page-for-binary fastx_reverse_complement
fastx_toolkit.x86_64: W: no-manual-page-for-binary fastq_to_fasta
fastx_toolkit.x86_64: W: no-manual-page-for-binary
fastx_nucleotide_distribution_graph.sh
fastx_toolkit.x86_64: W: no-manual-page-for-binary fastq_masker
fastx_toolkit.x86_64: W: no-manual-page-for-binary fastx_artifacts_filter
fastx_toolkit.x86_64: W: no-manual-page-for-binary fastx_uncollapser
fastx_toolkit.x86_64: W: no-manual-page-for-binary fastx_clipper
fastx_toolkit-debuginfo.x86_64: W: spelling-error Summary(en_US) fastx -> fast,
fasts, fast x
fastx_toolkit-debuginfo.x86_64: W: spelling-error %description -l en_US fastx
-> fast, fasts, fast x
fastx_toolkit-galaxy.x86_64: W: spelling-error Summary(en_US) fastx -> fast,
fasts, fast x
fastx_toolkit-galaxy.x86_64: W: spelling-error %description -l en_US fastx ->
fast, fasts, fast x
fastx_toolkit-galaxy.x86_64: W: spelling-error %description -l en_US
metagenomic -> meta genomic, meta-genomic, metagenesis
fastx_toolkit-galaxy.x86_64: W: no-documentation
4 packages and 0 specfiles checked; 0 errors, 30 warnings.

These are OK.

Most of the issues have been fixed. However, some still remain:

NEEDSWORK:
 - The -galaxy package contains autotools Makefiles. Get rid of them.
 - The license is AGPLv3+ as in libgtextutils.

[Bug 597307] Review Request: fastx_toolkit - Tools to process short-reads FASTA/FASTQ files

[Red Hat Bugzilla]

Please do not reply directly to this email. All additional
comments should be made in the comments box of this bug.

https://bugzilla.redhat.com/show_bug.cgi?id=597307

--- Comment #11 from Adam Huffman  2010-11-17 07:44:02 EST ---
New version at:

http://verdurin.fedorapeople.org/reviews/fastx_toolkit/fastx_toolkit.spec

http://verdurin.fedorapeople.org/reviews/fastx_toolkit/fastx_toolkit-0.0.13-...

[Bug 597307] Review Request: fastx_toolkit - Tools to process short-reads FASTA/FASTQ files

[Red Hat Bugzilla]

Please do not reply directly to this email. All additional
comments should be made in the comments box of this bug.

https://bugzilla.redhat.com/show_bug.cgi?id=597307

--- Comment #12 from Jussi Lehtola  2010-12-05 11:54:16 EST ---
Ping Adam, what's the status?

[Bug 597307] Review Request: fastx_toolkit - Tools to process short-reads FASTA/FASTQ files

[Red Hat Bugzilla]

Please do not reply directly to this email. All additional
comments should be made in the comments box of this bug.

https://bugzilla.redhat.com/show_bug.cgi?id=597307

Takanori MATSUURA  changed:

What    |Removed                     |Added
----------------------------------------------------------------------------
             Blocks|                            |663925

--- Comment #13 from Takanori MATSUURA  2010-12-17 06:42:07 EST ---
Autoconf-archive is now in review at bug 663925.

[Bug 597307] Review Request: fastx_toolkit - Tools to process short-reads FASTA/FASTQ files

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https://bugzilla.redhat.com/show_bug.cgi?id=597307

Takanori MATSUURA  changed:

What    |Removed                     |Added
----------------------------------------------------------------------------
             Blocks|663925                      |

[Bug 597307] Review Request: fastx_toolkit - Tools to process short-reads FASTA/FASTQ files

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--- Comment #14 from Adam Huffman  2011-03-22 07:32:49 EDT ---
Jussi,

Have you had a change to look at the latest version?

[Bug 597307] Review Request: fastx_toolkit - Tools to process short-reads FASTA/FASTQ files

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--- Comment #15 from Jussi Lehtola  2011-03-22 07:45:27 EDT ---
Crap, I had forgotten all about this review. Taking a look shortly.

[Bug 597307] Review Request: fastx_toolkit - Tools to process short-reads FASTA/FASTQ files

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Bug 597307 depends on bug 598511, which changed state.

Bug 598511 Summary: Review Request: libgtextutils - Assaf Gordon text utilities
https://bugzilla.redhat.com/show_bug.cgi?id=598511

What    |Old Value                   |New Value
----------------------------------------------------------------------------
         Resolution|                            |NEXTRELEASE
             Status|ASSIGNED                    |CLOSED

[Bug 597307] Review Request: fastx_toolkit - Tools to process short-reads FASTA/FASTQ files

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Jussi Lehtola  changed:

What    |Removed                     |Added
----------------------------------------------------------------------------
               Flag|fedora-review?              |fedora-review+

--- Comment #16 from Jussi Lehtola  2011-03-22 13:07:59 EDT ---
You're missing ownership of
 %{_datadir}/%{name}
It should be owned by -galaxy. Otherwise things should be fine.

Please fix the ownership before git import; what you need to do is change
 %{_datadir}/%{name}/galaxy/
to
 %{_datadir}/%{name}/
in -galaxy.

This package has been

APPROVED

[Bug 597307] Review Request: fastx_toolkit - Tools to process short-reads FASTA/FASTQ files

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Adam Huffman  changed:

What    |Removed                     |Added
----------------------------------------------------------------------------
               Flag|                            |fedora-cvs?

--- Comment #17 from Adam Huffman  2011-03-22 13:30:00 EDT ---
Many thanks for the review - I've made that last change in -4

New Package SCM Request
=======================
Package Name: fastx_toolkit
Short Description:  Tools to process short-reads FASTA/FASTQ files
Owners: verdurin
Branches: f14 f15 el5 el6
InitialCC:

[Bug 597307] Review Request: fastx_toolkit - Tools to process short-reads FASTA/FASTQ files

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--- Comment #18 from Jason Tibbitts  2011-03-22 13:51:58 EDT ---
Git done (by process-git-requests).

[Bug 597307] Review Request: fastx_toolkit - Tools to process short-reads FASTA/FASTQ files

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Adam Huffman  changed:

What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|ASSIGNED                    |CLOSED
         Resolution|                            |NEXTRELEASE
        Last Closed|                            |2011-04-07 17:40:36

[Bug 597307] Review Request: fastx_toolkit - Tools to process short-reads FASTA/FASTQ files

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Pierre-YvesChibon  changed:

What    |Removed                     |Added
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                 CC|                            |[e-mail]

--- Comment #19 from Pierre-YvesChibon  2011-05-25 08:15:37 EDT ---
Two month have past but nothing has been imported in the git.

[Bug 597307] Review Request: fastx_toolkit - Tools to process short-reads FASTA/FASTQ files

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--- Comment #20 from Adam Huffman  2011-05-27 06:35:38 EDT ---
Oops - I forgot to import the package...

Many thanks for spotting that.  Have just done so and submitted updates for all
four branches.