samtools: Use same openssl for host and run

[unode]

Not pinning openssl for runtime sometimes caused openssl-1.1 to be installed breaking samtools

Related to #12100 and #13903

ℹ️ :
Bioconda has finished the GCC7 migration. If you are dealing with C/C++ or Python package it can be that you need to rebuild other dependent packages. Bioconda utils - update-pinning will assist you with that. If you have any questions please use issue 13578.

---

• I have read the guidelines for bioconda recipes.
• This PR adds a new recipe.
• AFAIK, this recipe is directly relevant to the biological sciences (otherwise, please submit to the more general purpose conda-forge channel).
• This PR updates an existing recipe.
• This PR does something else (explain below).

[pb-cdunn]

Looks good. I'm eager to try this.

(GitHub was blocked, so I rebased onto master and force-pushed this. I'll try to merge after the re-test.)

[pb-cdunn]

Checking for ability to merge automatically…
Hang in there while we check the branch’s status.

I don't understand why this is sticking around. It seem trivial to merge. I'll try closing a competing samtools PR... Ah, that worked.

[pb-cdunn]

Note: One user found a work-around which involves installing specific versions of openssl and ncurses.

PacificBiosciences/pbbioconda#85

[unode]

#13903 was following the same road. Though this shouldn't be necessary.
Hopefully this was fixed in this pull request.

[pb-cdunn]

The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    cython-0.29.6              |   py27hf484d3e_0         2.1 MB  conda-forge
    minimap2-2.16              |       h84994c4_1         2.0 MB  bioconda
    pb-assembly-0.0.4          |           py27_5           4 KB  bioconda
    pb-falcon-0.2.6            |   py27hc0aa232_3         747 KB  bioconda
    samtools-1.9               |       h91753b0_5         636 KB  bioconda
    ------------------------------------------------------------
                                           Total:         5.5 MB

The following packages will be UPDATED:

  curl                                    7.64.0-h646f8bb_0 --> 7.64.0-h646f8bb_2
  cython                              0.29.5-py27hf484d3e_0 --> 0.29.6-py27hf484d3e_0
  krb5                                 1.16.3-hc83ff2d_1000 --> 1.16.3-h05b26f9_1001
  libcurl                                 7.64.0-h01ee5af_0 --> 7.64.0-h541490c_2
  libssh2                               1.8.0-h1ad7b7a_1003 --> 1.8.0-h90d6eec_1004
  minimap2                                  2.15-h84994c4_1 --> 2.16-h84994c4_1
  numpy                 1.16.1-py27_blas_openblash1522bff_0 --> 1.16.2-py27_blas_openblash1522bff_0
  openssl                                 1.0.2q-h14c3975_0 --> 1.1.1b-h14c3975_0
  pb-assembly                                  0.0.4-py27_4 --> 0.0.4-py27_5
  pb-falcon                            0.2.6-py27hc0aa232_1 --> 0.2.6-py27hc0aa232_3
  python                               2.7.15-h938d71a_1006 --> 2.7.15-h721da81_1008

The following packages will be DOWNGRADED:

  samtools                                   1.9-h57cc563_6 --> 1.9-h91753b0_5

Still no joy. I will rebuild pb-assembly and try again.

[unode]

I think this is what's causing the problem:

samtools                                   1.9-h57cc563_6 --> 1.9-h91753b0_5

It's downgrading samtools instead of upgrading it to 1.9-h91753b0_7.
I guess other tools are now depending on openssl-1.1 and conda is favoring that upgrade.
We'd probably need to mask or remove lower versions if we wanted to force this.

Alternatively checking which packages still build against openssl-1.0 and rebuilt all of them.
A bigger effort though.

[pb-cdunn]

% conda update --all
...
The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    cython-0.29.6              |   py27hf484d3e_0         2.1 MB  conda-forge
    minimap2-2.16              |       h84994c4_1         2.0 MB  bioconda
    pb-assembly-0.0.4          |           py27_6           4 KB  bioconda
    pb-falcon-0.2.6            |   py27hc0aa232_3         747 KB  bioconda
    samtools-1.9               |       h91753b0_5         636 KB  bioconda
    ------------------------------------------------------------
                                           Total:         5.5 MB

The following packages will be UPDATED:

  curl                                    7.64.0-h646f8bb_0 --> 7.64.0-h646f8bb_2
  cython                              0.29.5-py27hf484d3e_0 --> 0.29.6-py27hf484d3e_0
  krb5                                 1.16.3-hc83ff2d_1000 --> 1.16.3-h05b26f9_1001
  libcurl                                 7.64.0-h01ee5af_0 --> 7.64.0-h541490c_2
  libssh2                               1.8.0-h1ad7b7a_1003 --> 1.8.0-h90d6eec_1004
  minimap2                                  2.15-h84994c4_1 --> 2.16-h84994c4_1
  numpy                 1.16.1-py27_blas_openblash1522bff_0 --> 1.16.2-py27_blas_openblash1522bff_0
  openssl                                 1.0.2q-h14c3975_0 --> 1.1.1b-h14c3975_0
  pb-assembly                                  0.0.4-py27_4 --> 0.0.4-py27_6
  pb-falcon                            0.2.6-py27hc0aa232_1 --> 0.2.6-py27hc0aa232_3
  python                               2.7.15-h938d71a_1006 --> 2.7.15-h721da81_1008

The following packages will be DOWNGRADED:

  samtools                                   1.9-h57cc563_6 --> 1.9-h91753b0_5

% which samtools
~/.conda/envs/testa/bin/samtools
% ldd $(which samtools)
        linux-vdso.so.1 =>  (0x00007ffc33bee000)
        libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f217ca4c000)
        libz.so.1 => /home/UNIXHOME/cdunn/.conda/envs/testa/bin/../lib/libz.so.1 (0x00007f217ca31000)
        libm.so.6 => /lib64/libm.so.6 (0x00007f217c72f000)
        libbz2.so.1.0 => /home/UNIXHOME/cdunn/.conda/envs/testa/bin/../lib/libbz2.so.1.0 (0x00007f217c71b000)
        liblzma.so.5 => /home/UNIXHOME/cdunn/.conda/envs/testa/bin/../lib/liblzma.so.5 (0x00007f217c6f1000)
        libdeflate.so => /home/UNIXHOME/cdunn/.conda/envs/testa/bin/../lib/libdeflate.so (0x00007f217c6e1000)
        libcurl.so.4 => /home/UNIXHOME/cdunn/.conda/envs/testa/bin/../lib/libcurl.so.4 (0x00007f217c659000)
        libcrypto.so.1.0.0 => not found
        libncursesw.so.6 => /home/UNIXHOME/cdunn/.conda/envs/testa/bin/../lib/libncursesw.so.6 (0x00007f217c61c000)
        libtinfow.so.6 => /home/UNIXHOME/cdunn/.conda/envs/testa/bin/../lib/libtinfow.so.6 (0x00007f217c5df000)
        libc.so.6 => /lib64/libc.so.6 (0x00007f217c21b000)
        /lib64/ld-linux-x86-64.so.2 (0x000055fbcba44000)
        librt.so.1 => /lib64/librt.so.1 (0x00007f217c013000)
        libssh2.so.1 => /home/UNIXHOME/cdunn/.conda/envs/testa/bin/../lib/./libssh2.so.1 (0x00007f217bfe0000)
        libssl.so.1.1 => /home/UNIXHOME/cdunn/.conda/envs/testa/bin/../lib/./libssl.so.1.1 (0x00007f217bf4a000)
        libcrypto.so.1.1 => /home/UNIXHOME/cdunn/.conda/envs/testa/bin/../lib/./libcrypto.so.1.1 (0x00007f217bc52000)
        libgssapi_krb5.so.2 => /home/UNIXHOME/cdunn/.conda/envs/testa/bin/../lib/./libgssapi_krb5.so.2 (0x00007f217bc02000)
        libkrb5.so.3 => /home/UNIXHOME/cdunn/.conda/envs/testa/bin/../lib/./libkrb5.so.3 (0x00007f217bb26000)
        libk5crypto.so.3 => /home/UNIXHOME/cdunn/.conda/envs/testa/bin/../lib/./libk5crypto.so.3 (0x00007f217bb07000)
        libcom_err.so.3 => /home/UNIXHOME/cdunn/.conda/envs/testa/bin/../lib/./libcom_err.so.3 (0x00007f217bb00000)
        libdl.so.2 => /lib64/libdl.so.2 (0x00007f217b8fc000)
        libkrb5support.so.0 => /home/UNIXHOME/cdunn/.conda/envs/testa/bin/../lib/././libkrb5support.so.0 (0x00007f217b8ec000)
        libresolv.so.2 => /lib64/libresolv.so.2 (0x00007f217b6d2000)

ugh!