search

aquaskyline / SOAPdenovo2

Next generation sequencing reads de novo assembler.
GNU General Public License v3.0
220 stars 78 forks source link

binaries of newer versions #18

Closed KamilSJaron closed 7 years ago

KamilSJaron commented 7 years ago

I have some troubles to compile SOAPdenovo2. So, I wanted to give a try to pre-compiled binaries but I found only 3 years old binaries on source forge. Would it be possible to upload somewhere static binaries of newer versions? Thanks.

aquaskyline commented 7 years ago

which Linux distribution are you using?

KamilSJaron commented 7 years ago

CentOS release 6.8

aquaskyline commented 7 years ago

Binaries sent through email.

RE question can I host the binaries in Github.

I don’t think GitHub is the right place for binary, but thanks for your suggestion, I will find a way out.

BTW, there are two ways for you to install SOAPdenovo easily

  1. SOAPdenovo is a package in both Debian Med and RedHat, so you can install with command “apt-get install soapdenovo” or “yum install soapdenovo”.
  2. You can also install SOAPdenovo with Brew (Linuxbrew for Linux and Homebrew for Mac).
aersoares81 commented 7 years ago

Is there a new place for the binaries? I don't think they're available pre-compiled even if it says so on the main page.

aquaskyline commented 7 years ago

I suggest you to use bioconda to install SOAPdenovo

aersoares81 commented 7 years ago

I don't think I'm allowed to install bioconda on my cluster, could you please provide the binaries for the most recent version? The ones available on the sourceforge are outdated.

aquaskyline commented 7 years ago

bioconda can be installed in the user space, you don't need a root to do that.

On Mon, May 22, 2017 at 8:08 AM, Andre Soares notifications@github.com wrote:

I don't think I'm allowed to install bioconda on my cluster, could you please provide the binaries for the most recent version? The ones available on the sourceforge are outdated.

— You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub https://github.com/aquaskyline/SOAPdenovo2/issues/18#issuecomment-303081818, or mute the thread https://github.com/notifications/unsubscribe-auth/AA2pOQ2KUAKKtudoxKcitITy6iU8kBACks5r8XrMgaJpZM4MAedl .

-- Laurent

pliang64 commented 2 years ago

Hi Dr. Luo,

I wanted to install soapdenovo on my new Mac Studio, however, opposite to what is mentioned on the GitHub page, it's NOT available via brew. I tried to compile from the source code (r242), but it ran into too many error messages. By any chance you can make a binary version for me or guide me through the compilation? FYI, here is detailed OS ID: Darwin Kernel Version 21.5.0: Tue Apr 26 21:08:37 PDT 2022; root:xnu-8020.121.3~4/RELEASE_ARM64_T6000 x86_64.

I also have a question related to soapdeno regarding the discrepancy between the report on library and the specification in the configuration file. It seems that soapdenovo ignores the rd_len_cutoff setting at 151 and use the default of 100 bp. FYI, I have show below the content of the conf file and the error file regarding the library, and the SRR10035393 seq length is at 151 bp, and this was run on a Linux CentOS machine.

content of the configuration file (soap30x.conf)

[LIB] rd_len_cutoff=151 avg_ins=370 reverse_seq=0 asm_flags=3 rank=1 pair_num_cutoff=5 map_len=35 q1=SRR10035390_1.fastq.gz q2=SRR10035390_2.fastq.gz

report in the err file

Parameters: pregraph -s soap30x.conf -K 79 -p 40 -o soap30xd77

In soap30x.conf, 1 lib(s), maximum read length 100, maximum name length 256.

40 thread(s) initialized. ....... Time spent on hashing reads: 1767s, 619706556 read(s) processed. LIB(s) information: [LIB] 0, avg_ins 370, reverse 0.

end of error file

Is this just a bug in reporting or what it actually operated on? If it is latter, then I'd have to worry about losing 1/3 of the sequence data.

Thank you, Ping