bowtie2

[Jun Aruga]

Hi, I just share I am working on bowtie2 [1] packaging here [2] as a trial.

Because I have seen Debian Med(ical) team is using the mailing list to
share the package status, rather than a kind of issue page like
Pagure.

Right now it succeeded to build the bowtie2 RPM package on Fedora
rawhide x86_64.
As bowtie2 non-x86-64 packages needs simde [3] to build, I will do the
packaging too.

[1] https://github.com/BenLangmead/bowtie2
[2] https://github.com/junaruga/fedora-bowtie2
[3] https://github.com/nemequ/simde

-- 
Jun | He - His - Him

[Jun Aruga]

>  As bowtie2 non-x86-64 packages needs simde [3] to build, I will do
> the 
packaging too.

simde (SIMDe = SIMD Everywhere) is in review here.
https://bugzilla.redhat.com/show_bug.cgi?id=1823001

-- 
Jun | He - His - Him

[Jun Aruga]

For someone who wants to use bowtie2 latest version RPM.

The x86_64 and aarch64 binary RPMs for Fedora 33 are available here on Copr.
https://copr.fedorainfracloud.org/coprs/jaruga/staging/build/1334640/

As bowtie2 is shipped to the official repository, we need to wait
simde to be shipped at first.

Cheers,
Jun

-- 
Jun | He - His - Him

[Morgan Hough]

That’s great. What are the next couple packages you would like to see done?

On Sat, Apr 11, 2020 at 12:33 Jun Aruga <jaruga(a)redhat.com&gt; wrote:

>  For someone who wants to use bowtie2 latest version RPM.
>
>  The x86_64 and aarch64 binary RPMs for Fedora 33 are available here on
>  Copr.
>  https://copr.fedorainfracloud.org/coprs/jaruga/staging/build/1334640/
>
>  As bowtie2 is shipped to the official repository, we need to wait
>  simde to be shipped at first.
>
>  Cheers,
>  Jun
>
>  --
>  Jun | He - His - Him
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[Michel Alexandre Salim]

Apr 11, 2020 15:59:46 Morgan Hough <morgan.hough(a)gmail.com&gt;:

>  That’s great. What are the next couple packages you would like to see
> done?
>
>  
+1

Perhaps people can help either reviewing or submitting some of the needed packages?


-- 
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Michel Alexandre Salim
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[Jun Aruga]

>  As bowtie2 is shipped to the official repository, we need to wait
simde to be shipped at first.

Above is a typo.
We need to wait simde to be shipped at first for us to see that
bowtie2 is shipped to the official repository.

>  That’s great. What are the next couple packages you would like to see
> done? 
Hi Morgan and Michel,
I am glad you like it.

The packages are like this, though it might be changed.

* fastqc: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
* trinity: https://github.com/trinityrnaseq/trinityrnaseq
  required dependencies:
     * jellyfish: https://github.com/gmarcais/Jellyfish
     * salmon: https://github.com/COMBINE-lab/salmon
* igv: https://software.broadinstitute.org/software/igv/
* gatk: https://github.com/broadinstitute/gatk
* minimap: https://github.com/lh3/minimap
* miniasm: https://github.com/lh3/miniasm

Before that
* I want to fix the build failure [1] of bwa [2]
* I want to build htslib, samtools, vcftools on EPEL 7 and EPEL 8.

I wanted to check the necessary packages used in the following
nextflow pipeline project.
But right now the GitHub code has disappeared.
https://nf-co.re/covid19

* biogo: https://github.com/biogo/biogo might be my interest as it is
used in it.


>  Perhaps people can help either reviewing or submitting some of the
> needed packages? 
It's really helpful! Thanks.
Right now I need someone's review for simde that is a needed package
for bowtie2.


[1] https://koschei.fedoraproject.org/groups/biology
[2] https://src.fedoraproject.org/rpms/bwa/pull-request/1



--
Jun | He - His - Him

[Jun Aruga]

simde is available on Fedora rawhide.
https://src.fedoraproject.org/rpms/simde

And could anyone review the bowtie2 package? I just opened the ticket.
The bowtie2 package is going to be available on x86_64, aarch64 and ppc64le.

Review Request: bowtie2 - A read aligner for genome sequencing
https://bugzilla.redhat.com/show_bug.cgi?id=1824348

Thanks.

-- 
Jun | He - His - Him

[Jun Aruga]

>  Review Request: bowtie2 - A read aligner for genome sequencing
>  https://bugzilla.redhat.com/show_bug.cgi?id=1824348 
It is great to see that someone took a casual review forthe ticket.
Now I need someone's help to get the review approved.

-- 
Jun | He - His - Him

[Jun Aruga]

bowtie2 rawhide was released,  and the older Fedoras and EPEL 8 and 7
versions are going to be released maybe in 1 week, as they exist in
Bodhi.
https://src.fedoraproject.org/rpms/bowtie2
Thanks for your help!

>  Before that
>  * I want to fix the build failure [1] of bwa [2]
>  * I want to build htslib, samtools, vcftools on EPEL 7 and EPEL 8. 
The above task is also done for now.
* bwa: fixed, and the latest version for EPEL8 and EPEL7 builds are in Bodhi.
* htslib, samtools: the latest version for EPEL8 and EPEL7 builds are in Bodhi.
* vcftools: EPEL7: already available, EPEL8: asking here.
https://bugzilla.redhat.com/show_bug.cgi?id=1833324

>  I wanted to check the necessary packages used in the following
>  nextflow pipeline project.
>  But right now the GitHub code has disappeared.
>  https://nf-co.re/covid19 
As a note, the project https://nf-co.re/covid19 was moved to
nf-core/artic and nf-core/viralrecon.

Cheers,
Jun

-- 
Jun | He - His - Him