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dstreett / FLASH2

Flash2 has some improvements from flash_1 including new logic from innie and outie overlaps as well as some initial steps for flash for amplicons
GNU General Public License v3.0
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problem with creating conda env with flash2 #10

Open balathl opened 6 years ago

balathl commented 6 years ago

Hi,

I am trying to build a pipeline which includes flash2. The git available for flash2 currently has some issues. Is it possible to provide a tarball for flash2 which can be used to include in conda env as below:

https://conda.io/docs/user-guide/tutorials/build-pkgs.html

The attempts that i made were: conda-build flash2 Adding in variants from internal_defaults INFO:conda_build.variants:Adding in variants from internal_defaults Attempting to finalize metadata for flash2 INFO:conda_build.metadata:Attempting to finalize metadata for flash2 BUILD START: [u'flash2-2.2.00-0.tar.bz2'] Cloning into '/root/anaconda/conda-bld/flash2_1517590357585/work'... done. checkout: u'v2.2.00' error: pathspec 'v2.2.00' did not match any file(s) known to git. Warning: failed to download source. If building, will try again after downloading recipe dependencies. Error was: Command '['/usr/bin/git', 'checkout', 'v2.2.00']' returned non-zero exit status 1 Failed to download or patch source. Please see build log for info.

Below is my meta.yaml file content: ################## meta.yaml ################################## package: name: flash2 version: "2.2.00"

source: git_rev: v2.2.00 git_url: https://github.com/dstreett/FLASH2.git

requirements: build:

run:

test: imports:

about: home: https://github.com/dstreett/FLASH2 license: BSD license_file: LICENSE ######################build.sh################################# $PYTHON setup.py install --single-version-externally-managed --record=record.txt # Python command to install the script. ######################bld.bat################################### "%PYTHON%" setup.py install --single-version-externally-managed --record=record.txt if errorlevel 1 exit 1

All the above three files were in flash2 folder created and the command executed was:

conda-build flash2

Error i got is below:

Adding in variants from internal_defaults INFO:conda_build.variants:Adding in variants from internal_defaults Attempting to finalize metadata for flash2 INFO:conda_build.metadata:Attempting to finalize metadata for flash2 BUILD START: [u'flash2-2.2.00-0.tar.bz2'] Cloning into '/root/anaconda/conda-bld/flash2_1517590750211/work'... done. checkout: u'v2.2.00' error: pathspec 'v2.2.00' did not match any file(s) known to git. Warning: failed to download source. If building, will try again after downloading recipe dependencies. Error was: Command '['/usr/bin/git', 'checkout', 'v2.2.00']' returned non-zero exit status 1 Failed to download or patch source. Please see build log for info.

Hope you can help to make flash2 available/compatible with conda env!!

Bala

msettles commented 6 years ago

Hello Bala,

I have no idea what this entails, but I took a guess that its looking for a release and so I’ve created one. You may need to change the version to 2.2.00 dropping the ‘v’.

But give it try and let us know

Matt

From: balathl notifications@github.com Reply-To: dstreett/FLASH2 reply@reply.github.com Date: Tuesday, February 6, 2018 at 11:22 PM To: dstreett/FLASH2 FLASH2@noreply.github.com Cc: Subscribed subscribed@noreply.github.com Subject: [dstreett/FLASH2] problem with creating conda env with flash2 (#10)

Hi,

I am trying to build a pipeline which includes flash2. The git available for flash2 currently has some issues. Is it possible to provide a tarball for flash2 which can be used to include in conda env as below:

https://conda.io/docs/user-guide/tutorials/build-pkgs.html

The attempts that i made were: conda-build flash2 Adding in variants from internal_defaults INFO:conda_build.variants:Adding in variants from internal_defaults Attempting to finalize metadata for flash2 INFO:conda_build.metadata:Attempting to finalize metadata for flash2 BUILD START: [u'flash2-2.2.00-0.tar.bz2'] Cloning into '/root/anaconda/conda-bld/flash2_1517590357585/work'... done. checkout: u'v2.2.00' error: pathspec 'v2.2.00' did not match any file(s) known to git. Warning: failed to download source. If building, will try again after downloading recipe dependencies. Error was: Command '['/usr/bin/git', 'checkout', 'v2.2.00']' returned non-zero exit status 1 Failed to download or patch source. Please see build log for info.

Below is my meta.yaml file content: ################## meta.yaml ################################## package: name: flash2 version: "2.2.00"

source: git_rev: v2.2.00 git_url: https://github.com/dstreett/FLASH2.git

requirements: build:

run:

test: imports:

about: home: https://github.com/dstreett/FLASH2 license: BSD license_file: LICENSE ######################build.sh################################# $PYTHON setup.py install --single-version-externally-managed --record=record.txt # Python command to install the script. ######################bld.bat################################### "%PYTHON%" setup.py install --single-version-externally-managed --record=record.txt if errorlevel 1 exit 1

All the above three files were in flash2 folder created and the command executed was:

conda-build flash2

Error i got is below:

Adding in variants from internal_defaults INFO:conda_build.variants:Adding in variants from internal_defaults Attempting to finalize metadata for flash2 INFO:conda_build.metadata:Attempting to finalize metadata for flash2 BUILD START: [u'flash2-2.2.00-0.tar.bz2'] Cloning into '/root/anaconda/conda-bld/flash2_1517590750211/work'... done. checkout: u'v2.2.00' error: pathspec 'v2.2.00' did not match any file(s) known to git. Warning: failed to download source. If building, will try again after downloading recipe dependencies. Error was: Command '['/usr/bin/git', 'checkout', 'v2.2.00']' returned non-zero exit status 1 Failed to download or patch source. Please see build log for info.

Hope you can help to make flash2 available/compatible with conda env!!

Bala

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.

balathl commented 6 years ago

Hi,

Thanks for your quick response! I rerun the code but now ended up in slightly different error as below:

conda-build flash2

Adding in variants from internal_defaults INFO:conda_build.variants:Adding in variants from internal_defaults Attempting to finalize metadata for flash2 INFO:conda_build.metadata:Attempting to finalize metadata for flash2 BUILD START: [u'flash2-2.2.00-0.tar.bz2'] From https://github.com/dstreett/FLASH2

You are in 'detached HEAD' state. You can look around, make experimental changes and commit them, and you can discard any commits you make in this state without impacting any branches by performing another checkout.

If you want to create a new branch to retain commits you create, you may do so (now or later) by using -b with the checkout command again. Example:

git checkout -b new_branch_name

HEAD is now at 64826f4... Merge pull request #7 from dstreett/develop ==> git log -n1 <==

commit 64826f4574b11b3c0ae7460826f30be16f49c3ea Merge: 55e230f 288e1f0 Author: David Streett davidastreett@hotmail.com<mailto:davidastreett@hotmail.com> Date: Fri May 6 15:45:53 2016 -0700

Merge pull request #7 from dstreett/develop

Develop

==> git describe --tags --dirty <==

2.2.00

==> git status <==

HEAD detached at 2.2.00 nothing to commit, working directory clean

source tree in: /root/anaconda/conda-bld/flash2_1518095364537/work /root/anaconda/conda-bld/flash2_1518095364537/work/conda_build.sh: line 56: setup.py: command not found Traceback (most recent call last): File "/root/anaconda/bin/conda-build", line 11, in sys.exit(main()) File "/root/anaconda/lib/python2.7/site-packages/conda_build/cli/main_build.py", line 413, in main execute(sys.argv[1:]) File "/root/anaconda/lib/python2.7/site-packages/conda_build/cli/main_build.py", line 404, in execute verify=args.verify) File "/root/anaconda/lib/python2.7/site-packages/conda_build/api.py", line 193, in build need_source_download=need_source_download, config=config, variants=variants) File "/root/anaconda/lib/python2.7/site-packages/conda_build/build.py", line 1944, in build_tree notest=notest, File "/root/anaconda/lib/python2.7/site-packages/conda_build/build.py", line 1240, in build utils.check_call_env(cmd, env=env, cwd=src_dir) File "/root/anaconda/lib/python2.7/site-packages/conda_build/utils.py", line 678, in check_call_env return _func_defaulting_env_to_os_environ(subprocess.check_call, *popenargs, kwargs) File "/root/anaconda/lib/python2.7/site-packages/conda_build/utils.py", line 674, in _func_defaulting_env_to_os_environ return func(_args, kwargs) File "/root/anaconda/lib/python2.7/subprocess.py", line 541, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '['/bin/bash', '-e', '/root/anaconda/conda-bld/flash2_1518095364537/work/conda_build.sh']' returned non-zero exit status 127

I tried to contact the conda developer as well as it might be from conda as well. But if you think the error might be from your side then feel free to provide some solution.

Best Regards, Bala

From: Matt Settles [notifications@github.com] Sent: Wednesday, February 07, 2018 8:29 PM To: dstreett/FLASH2 Cc: Jayaprakash Balamuralikrishna; Author Subject: Re: [dstreett/FLASH2] problem with creating conda env with flash2 (#10)

Hello Bala,

I have no idea what this entails, but I took a guess that its looking for a release and so I’ve created one. You may need to change the version to 2.2.00 dropping the ‘v’.

But give it try and let us know

Matt

From: balathl notifications@github.com Reply-To: dstreett/FLASH2 reply@reply.github.com Date: Tuesday, February 6, 2018 at 11:22 PM To: dstreett/FLASH2 FLASH2@noreply.github.com Cc: Subscribed subscribed@noreply.github.com Subject: [dstreett/FLASH2] problem with creating conda env with flash2 (#10)

Hi,

I am trying to build a pipeline which includes flash2. The git available for flash2 currently has some issues. Is it possible to provide a tarball for flash2 which can be used to include in conda env as below:

https://conda.io/docs/user-guide/tutorials/build-pkgs.html

The attempts that i made were: conda-build flash2 Adding in variants from internal_defaults INFO:conda_build.variants:Adding in variants from internal_defaults Attempting to finalize metadata for flash2 INFO:conda_build.metadata:Attempting to finalize metadata for flash2 BUILD START: [u'flash2-2.2.00-0.tar.bz2'] Cloning into '/root/anaconda/conda-bld/flash2_1517590357585/work'... done. checkout: u'v2.2.00' error: pathspec 'v2.2.00' did not match any file(s) known to git. Warning: failed to download source. If building, will try again after downloading recipe dependencies. Error was: Command '['/usr/bin/git', 'checkout', 'v2.2.00']' returned non-zero exit status 1 Failed to download or patch source. Please see build log for info.

Below is my meta.yaml file content: ################## meta.yaml ################################## package: name: flash2 version: "2.2.00"

source: git_rev: v2.2.00 git_url: https://github.com/dstreett/FLASH2.git

requirements: build:

run:

test: imports:

about: home: https://github.com/dstreett/FLASH2 license: BSD license_file: LICENSE ######################build.sh################################# $PYTHON setup.py install --single-version-externally-managed --record=record.txt # Python command to install the script. ######################bld.bat################################### "%PYTHON%" setup.py install --single-version-externally-managed --record=record.txt if errorlevel 1 exit 1

All the above three files were in flash2 folder created and the command executed was:

conda-build flash2

Error i got is below:

Adding in variants from internal_defaults INFO:conda_build.variants:Adding in variants from internal_defaults Attempting to finalize metadata for flash2 INFO:conda_build.metadata:Attempting to finalize metadata for flash2 BUILD START: [u'flash2-2.2.00-0.tar.bz2'] Cloning into '/root/anaconda/conda-bld/flash2_1517590750211/work'... done. checkout: u'v2.2.00' error: pathspec 'v2.2.00' did not match any file(s) known to git. Warning: failed to download source. If building, will try again after downloading recipe dependencies. Error was: Command '['/usr/bin/git', 'checkout', 'v2.2.00']' returned non-zero exit status 1 Failed to download or patch source. Please see build log for info.

Hope you can help to make flash2 available/compatible with conda env!!

Bala

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/dstreett/FLASH2/issues/10#issuecomment-363864523, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AcX5gnCxXa7h9X2kjbCl-Yt8irIz5q_Zks5tSeuWgaJpZM4R8QFO.

msettles commented 6 years ago

Bala, I use Anaconda to manage my python environment, flash2 is C code, 0 python what I see below is that conda-build is looking for setup.py a file used to build python programs. so it may be that conda-build it's intended only gl for python apps (I know nothing about comda-build) and it's not for c programs.

if the developers say otherwise and propose a solution let me knew.

Matt

On Feb 8, 2018 2:22 AM, "balathl" notifications@github.com wrote:

Hi,

Thanks for your quick response! I rerun the code but now ended up in slightly different error as below:

conda-build flash2

Adding in variants from internal_defaults INFO:conda_build.variants:Adding in variants from internal_defaults Attempting to finalize metadata for flash2 INFO:conda_build.metadata:Attempting to finalize metadata for flash2 BUILD START: [u'flash2-2.2.00-0.tar.bz2'] From https://github.com/dstreett/FLASH2

You are in 'detached HEAD' state. You can look around, make experimental changes and commit them, and you can discard any commits you make in this state without impacting any branches by performing another checkout.

If you want to create a new branch to retain commits you create, you may do so (now or later) by using -b with the checkout command again. Example:

git checkout -b new_branch_name

HEAD is now at 64826f4... Merge pull request #7 from dstreett/develop ==> git log -n1 <==

commit 64826f4574b11b3c0ae7460826f30be16f49c3ea Merge: 55e230f 288e1f0 Author: David Streett <davidastreett@hotmail.com<mailto: davidastreett@hotmail.com>> Date: Fri May 6 15:45:53 2016 -0700

Merge pull request #7 from dstreett/develop

Develop

==> git describe --tags --dirty <==

2.2.00

==> git status <==

HEAD detached at 2.2.00 nothing to commit, working directory clean

source tree in: /root/anaconda/conda-bld/flash2_1518095364537/work /root/anaconda/conda-bld/flash2_1518095364537/work/conda_build.sh: line 56: setup.py: command not found Traceback (most recent call last): File "/root/anaconda/bin/conda-build", line 11, in sys.exit(main()) File "/root/anaconda/lib/python2.7/site-packages/conda_build/cli/main_build.py", line 413, in main execute(sys.argv[1:]) File "/root/anaconda/lib/python2.7/site-packages/conda_build/cli/main_build.py", line 404, in execute verify=args.verify) File "/root/anaconda/lib/python2.7/site-packages/conda_build/api.py", line 193, in build need_source_download=need_source_download, config=config, variants=variants) File "/root/anaconda/lib/python2.7/site-packages/conda_build/build.py", line 1944, in build_tree notest=notest, File "/root/anaconda/lib/python2.7/site-packages/conda_build/build.py", line 1240, in build utils.check_call_env(cmd, env=env, cwd=src_dir) File "/root/anaconda/lib/python2.7/site-packages/conda_build/utils.py", line 678, in check_call_env return _func_defaulting_env_to_os_environ(subprocess.check_call, *popenargs, kwargs) File "/root/anaconda/lib/python2.7/site-packages/conda_build/utils.py", line 674, in _func_defaulting_env_to_os_environ return func(_args, kwargs) File "/root/anaconda/lib/python2.7/subprocess.py", line 541, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '['/bin/bash', '-e', '/root/anaconda/conda-bld/flash2_1518095364537/work/conda_build.sh']' returned non-zero exit status 127

I tried to contact the conda developer as well as it might be from conda as well. But if you think the error might be from your side then feel free to provide some solution.

Best Regards, Bala

From: Matt Settles [notifications@github.com] Sent: Wednesday, February 07, 2018 8:29 PM To: dstreett/FLASH2 Cc: Jayaprakash Balamuralikrishna; Author Subject: Re: [dstreett/FLASH2] problem with creating conda env with flash2 (#10)

Hello Bala,

I have no idea what this entails, but I took a guess that its looking for a release and so I’ve created one. You may need to change the version to 2.2.00 dropping the ‘v’.

But give it try and let us know

Matt

From: balathl notifications@github.com Reply-To: dstreett/FLASH2 reply@reply.github.com

Date: Tuesday, February 6, 2018 at 11:22 PM To: dstreett/FLASH2 FLASH2@noreply.github.com Cc: Subscribed subscribed@noreply.github.com Subject: [dstreett/FLASH2] problem with creating conda env with flash2 (#10)

Hi,

I am trying to build a pipeline which includes flash2. The git available for flash2 currently has some issues. Is it possible to provide a tarball for flash2 which can be used to include in conda env as below:

https://conda.io/docs/user-guide/tutorials/build-pkgs.html

The attempts that i made were: conda-build flash2 Adding in variants from internal_defaults INFO:conda_build.variants:Adding in variants from internal_defaults Attempting to finalize metadata for flash2 INFO:conda_build.metadata:Attempting to finalize metadata for flash2 BUILD START: [u'flash2-2.2.00-0.tar.bz2'] Cloning into '/root/anaconda/conda-bld/flash2_1517590357585/work'... done. checkout: u'v2.2.00' error: pathspec 'v2.2.00' did not match any file(s) known to git. Warning: failed to download source. If building, will try again after downloading recipe dependencies. Error was: Command '['/usr/bin/git', 'checkout', 'v2.2.00']' returned non-zero exit status 1 Failed to download or patch source. Please see build log for info.

Below is my meta.yaml file content: ################## meta.yaml ################################## package: name: flash2 version: "2.2.00"

source: git_rev: v2.2.00 git_url: https://github.com/dstreett/FLASH2.git

requirements: build:

run:

test: imports:

about: home: https://github.com/dstreett/FLASH2 license: BSD license_file: LICENSE ######################build.sh################################# $PYTHON setup.py install --single-version-externally-managed --record=record.txt # Python command to install the script. ######################bld.bat################################### "%PYTHON%" setup.py install --single-version-externally-managed --record=record.txt if errorlevel 1 exit 1

All the above three files were in flash2 folder created and the command executed was:

conda-build flash2

Error i got is below:

Adding in variants from internal_defaults INFO:conda_build.variants:Adding in variants from internal_defaults Attempting to finalize metadata for flash2 INFO:conda_build.metadata:Attempting to finalize metadata for flash2 BUILD START: [u'flash2-2.2.00-0.tar.bz2'] Cloning into '/root/anaconda/conda-bld/flash2_1517590750211/work'... done. checkout: u'v2.2.00' error: pathspec 'v2.2.00' did not match any file(s) known to git. Warning: failed to download source. If building, will try again after downloading recipe dependencies. Error was: Command '['/usr/bin/git', 'checkout', 'v2.2.00']' returned non-zero exit status 1 Failed to download or patch source. Please see build log for info.

Hope you can help to make flash2 available/compatible with conda env!!

Bala

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/ dstreett/FLASH2/issues/10#issuecomment-363864523, or mute the thread< https://github.com/notifications/unsubscribe-auth/AcX5gnCxXa7h9X2kjbCl- Yt8irIz5q_Zks5tSeuWgaJpZM4R8QFO>.

— You are receiving this because you commented.

Reply to this email directly, view it on GitHub https://github.com/dstreett/FLASH2/issues/10#issuecomment-364067466, or mute the thread https://github.com/notifications/unsubscribe-auth/AAno5r7KTyzPAqzrbQmC6y65aBSPYPkCks5tSsrOgaJpZM4R8QFO .

balathl commented 6 years ago

Dear Matt,

I made the flash2 available in anaconda with your release with the below code. Now it can be integrated into some pipelines easily with conda env too. Thanks for your quick response on the release.

##################################################################################### cat meta.yaml {% set name = "flash2" %} {% set version = "2.2.00" %} {% set build = 0 %} {% set hash = "7bb357a935de87be8a294b35ed281eca2e08afa1e1a1d1b1c24a024b80b713ff" %}

package: name: {{ name }} version: {{ version }}

source: fn: {{ name }}-{{ version}}.tar.gz url: https://github.com/dstreett/FLASH2/archive/{{ version }}.tar.gz sha256: {{ hash }}

build: number: {{ build }} script: make

requirements: build:

test: commands:

about: home: https://github.com/dstreett/FLASH2 summary: FLASH is a tool to merge paired-end reads generated from DNA fragments

license: [the repos license (which doesn't exist)]

license_file: [you should create a LICENSE file since the repo has none]

conda-build flash2 #flash2 is folder containing meta.yaml file

anaconda upload /root/anaconda/conda-bld/linux-64/flash2-2.2.00-0.tar.bz2

####################################################################################

Bala

From: Matt Settles [notifications@github.com] Sent: Thursday, February 08, 2018 10:07 PM To: dstreett/FLASH2 Cc: Jayaprakash Balamuralikrishna; Author Subject: Re: [dstreett/FLASH2] problem with creating conda env with flash2 (#10)

Bala, I use Anaconda to manage my python environment, flash2 is C code, 0 python what I see below is that conda-build is looking for setup.py a file used to build python programs. so it may be that conda-build it's intended only gl for python apps (I know nothing about comda-build) and it's not for c programs.

if the developers say otherwise and propose a solution let me knew.

Matt

On Feb 8, 2018 2:22 AM, "balathl" notifications@github.com wrote:

Hi,

Thanks for your quick response! I rerun the code but now ended up in slightly different error as below:

conda-build flash2

Adding in variants from internal_defaults INFO:conda_build.variants:Adding in variants from internal_defaults Attempting to finalize metadata for flash2 INFO:conda_build.metadata:Attempting to finalize metadata for flash2 BUILD START: [u'flash2-2.2.00-0.tar.bz2'] From https://github.com/dstreett/FLASH2

You are in 'detached HEAD' state. You can look around, make experimental changes and commit them, and you can discard any commits you make in this state without impacting any branches by performing another checkout.

If you want to create a new branch to retain commits you create, you may do so (now or later) by using -b with the checkout command again. Example:

git checkout -b new_branch_name

HEAD is now at 64826f4... Merge pull request #7 from dstreett/develop ==> git log -n1 <==

commit 64826f4574b11b3c0ae7460826f30be16f49c3ea Merge: 55e230f 288e1f0 Author: David Streett <davidastreett@hotmail.com<mailto: davidastreett@hotmail.com>> Date: Fri May 6 15:45:53 2016 -0700

Merge pull request #7 from dstreett/develop

Develop

==> git describe --tags --dirty <==

2.2.00

==> git status <==

HEAD detached at 2.2.00 nothing to commit, working directory clean

source tree in: /root/anaconda/conda-bld/flash2_1518095364537/work /root/anaconda/conda-bld/flash2_1518095364537/work/conda_build.sh: line 56: setup.py: command not found Traceback (most recent call last): File "/root/anaconda/bin/conda-build", line 11, in sys.exit(main()) File "/root/anaconda/lib/python2.7/site-packages/conda_build/cli/main_build.py", line 413, in main execute(sys.argv[1:]) File "/root/anaconda/lib/python2.7/site-packages/conda_build/cli/main_build.py", line 404, in execute verify=args.verify) File "/root/anaconda/lib/python2.7/site-packages/conda_build/api.py", line 193, in build need_source_download=need_source_download, config=config, variants=variants) File "/root/anaconda/lib/python2.7/site-packages/conda_build/build.py", line 1944, in build_tree notest=notest, File "/root/anaconda/lib/python2.7/site-packages/conda_build/build.py", line 1240, in build utils.check_call_env(cmd, env=env, cwd=src_dir) File "/root/anaconda/lib/python2.7/site-packages/conda_build/utils.py", line 678, in check_call_env return _func_defaulting_env_to_os_environ(subprocess.check_call, *popenargs, kwargs) File "/root/anaconda/lib/python2.7/site-packages/conda_build/utils.py", line 674, in _func_defaulting_env_to_os_environ return func(_args, kwargs) File "/root/anaconda/lib/python2.7/subprocess.py", line 541, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '['/bin/bash', '-e', '/root/anaconda/conda-bld/flash2_1518095364537/work/conda_build.sh']' returned non-zero exit status 127

I tried to contact the conda developer as well as it might be from conda as well. But if you think the error might be from your side then feel free to provide some solution.

Best Regards, Bala

From: Matt Settles [notifications@github.com] Sent: Wednesday, February 07, 2018 8:29 PM To: dstreett/FLASH2 Cc: Jayaprakash Balamuralikrishna; Author Subject: Re: [dstreett/FLASH2] problem with creating conda env with flash2 (#10)

Hello Bala,

I have no idea what this entails, but I took a guess that its looking for a release and so I’ve created one. You may need to change the version to 2.2.00 dropping the ‘v’.

But give it try and let us know

Matt

From: balathl notifications@github.com Reply-To: dstreett/FLASH2 reply@reply.github.com

Date: Tuesday, February 6, 2018 at 11:22 PM To: dstreett/FLASH2 FLASH2@noreply.github.com Cc: Subscribed subscribed@noreply.github.com Subject: [dstreett/FLASH2] problem with creating conda env with flash2 (#10)

Hi,

I am trying to build a pipeline which includes flash2. The git available for flash2 currently has some issues. Is it possible to provide a tarball for flash2 which can be used to include in conda env as below:

https://conda.io/docs/user-guide/tutorials/build-pkgs.html

The attempts that i made were: conda-build flash2 Adding in variants from internal_defaults INFO:conda_build.variants:Adding in variants from internal_defaults Attempting to finalize metadata for flash2 INFO:conda_build.metadata:Attempting to finalize metadata for flash2 BUILD START: [u'flash2-2.2.00-0.tar.bz2'] Cloning into '/root/anaconda/conda-bld/flash2_1517590357585/work'... done. checkout: u'v2.2.00' error: pathspec 'v2.2.00' did not match any file(s) known to git. Warning: failed to download source. If building, will try again after downloading recipe dependencies. Error was: Command '['/usr/bin/git', 'checkout', 'v2.2.00']' returned non-zero exit status 1 Failed to download or patch source. Please see build log for info.

Below is my meta.yaml file content: ################## meta.yaml ################################## package: name: flash2 version: "2.2.00"

source: git_rev: v2.2.00 git_url: https://github.com/dstreett/FLASH2.git

requirements: build:

run:

test: imports:

about: home: https://github.com/dstreett/FLASH2 license: BSD license_file: LICENSE ######################build.sh################################# $PYTHON setup.py install --single-version-externally-managed --record=record.txt # Python command to install the script. ######################bld.bat################################### "%PYTHON%" setup.py install --single-version-externally-managed --record=record.txt if errorlevel 1 exit 1

All the above three files were in flash2 folder created and the command executed was:

conda-build flash2

Error i got is below:

Adding in variants from internal_defaults INFO:conda_build.variants:Adding in variants from internal_defaults Attempting to finalize metadata for flash2 INFO:conda_build.metadata:Attempting to finalize metadata for flash2 BUILD START: [u'flash2-2.2.00-0.tar.bz2'] Cloning into '/root/anaconda/conda-bld/flash2_1517590750211/work'... done. checkout: u'v2.2.00' error: pathspec 'v2.2.00' did not match any file(s) known to git. Warning: failed to download source. If building, will try again after downloading recipe dependencies. Error was: Command '['/usr/bin/git', 'checkout', 'v2.2.00']' returned non-zero exit status 1 Failed to download or patch source. Please see build log for info.

Hope you can help to make flash2 available/compatible with conda env!!

Bala

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